{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T18:58:11Z","timestamp":1789585091634,"version":"build-2803163510"},"reference-count":106,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,11,25]],"date-time":"2024-11-25T00:00:00Z","timestamp":1732492800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,11,25]],"date-time":"2024-11-25T00:00:00Z","timestamp":1732492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Cell Discov"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Promyelocytic leukemia protein (PML) nuclear bodies (NBs) are essential in regulating tumor suppression, antiviral response, inflammation, metabolism, aging, and other important life processes. The re-assembly of PML NBs might lead to an ~100% cure of acute promyelocytic leukemia. However, until now, the molecular mechanism underpinning PML NB biogenesis remains elusive due to the lack of structural information. In this study, we present the cryo-electron microscopy (cryo-EM) structure of the PML dimer at an overall resolution of 5.3\u2009\u00c5, encompassing the RING, B-box1\/2 and part of the coiled-coil (RBCC) domains. The integrated approach, combining crosslinking and mass spectrometry (XL-MS) and functional analyses, enabled us to observe a unique folding event within the RBCC domains. The RING and B-box1\/2 domains fold around the \u03b13 helix, and the \u03b16 helix serves as a pivotal interface for PML dimerization. More importantly, further characterizations of the cryo-EM structure in conjugation with AlphaFold2 prediction, XL-MS, and NB formation assays, help unveil an unprecedented octopus-like mechanism in NB assembly, wherein each CC helix of a PML dimer (PML dimer A) interacts with a CC helix from a neighboring PML dimer (PML dimer B) in an anti-parallel configuration, ultimately leading to the formation of a 2\u2009\u00b5m membrane-less subcellular organelle.<\/jats:p>","DOI":"10.1038\/s41421-024-00735-3","type":"journal-article","created":{"date-parts":[[2024,11,25]],"date-time":"2024-11-25T12:47:45Z","timestamp":1732538865000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Cryo-EM structure of PML RBCC dimer reveals CC-mediated octopus-like nuclear body assembly mechanism"],"prefix":"10.1038","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4419-5180","authenticated-orcid":false,"given":"Yangxia","family":"Tan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiawei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonglei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyi","family":"Zhuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodan","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7693-3910","authenticated-orcid":false,"given":"Yue","family":"Yin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanling","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7164-8694","authenticated-orcid":false,"given":"Yao","family":"Cong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7904-2382","authenticated-orcid":false,"given":"Guoyu","family":"Meng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,11,25]]},"reference":[{"key":"735_CR1","doi-asserted-by":"publisher","first-page":"167976","DOI":"10.1016\/j.jmb.2023.167976","volume":"435","author":"GL Boccaccio","year":"2023","unstructured":"Boccaccio, G. L., Thomas, M. G. & Garc\u00eda, C. C. Membraneless organelles and condensates orchestrate innate immunity against viruses. J. Mol. Biol. 435, 167976 (2023).","journal-title":"J. Mol. Biol."},{"key":"735_CR2","doi-asserted-by":"publisher","first-page":"11007","DOI":"10.3390\/ijms241311007","volume":"24","author":"YI Mokin","year":"2023","unstructured":"Mokin, Y. I. et al. Nucleolar- and nuclear-stress-induced membrane-less organelles: a proteome analysis through the prism of liquid-liquid phase separation. Int. J. Mol. Sci. 24, 11007 (2023).","journal-title":"Int. J. Mol. Sci."},{"key":"735_CR3","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1038\/s41586-020-1982-9","volume":"578","author":"S Yasuda","year":"2020","unstructured":"Yasuda, S. et al. Stress- and ubiquitylation-dependent phase separation of the proteasome. Nature 578, 296\u2013300 (2020).","journal-title":"Nature"},{"key":"735_CR4","doi-asserted-by":"publisher","DOI":"10.1126\/science.aao5654","volume":"359","author":"TM Franzmann","year":"2018","unstructured":"Franzmann, T. M. et al. Phase separation of a yeast prion protein promotes cellular fitness. Science 359, eaao5654 (2018).","journal-title":"Science"},{"key":"735_CR5","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.1016\/j.cell.2017.02.027","volume":"168","author":"JA Riback","year":"2017","unstructured":"Riback, J. A. et al. Stress-triggered phase separation is an adaptive, evolutionarily tuned response. Cell 168, 1028\u20131040.e19 (2017).","journal-title":"Cell"},{"key":"735_CR6","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1038\/nri2413","volume":"8","author":"K Ozato","year":"2008","unstructured":"Ozato, K., Shin, D. M., Chang, T. H. & Morse, H. C. 3rd TRIM family proteins and their emerging roles in innate immunity. Nat. Rev. Immunol. 8, 849\u2013860 (2008).","journal-title":"Nat. Rev. Immunol."},{"key":"735_CR7","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1002\/bies.20304","volume":"27","author":"G Meroni","year":"2005","unstructured":"Meroni, G. & Diez-Roux, G. TRIM\/RBCC, a novel class of \u2018single protein RING finger\u2019 E3 ubiquitin ligases. Bioessays 27, 1147\u20131157 (2005).","journal-title":"Bioessays"},{"key":"735_CR8","doi-asserted-by":"publisher","first-page":"2140","DOI":"10.1093\/emboj\/20.9.2140","volume":"20","author":"A Reymond","year":"2001","unstructured":"Reymond, A. et al. The tripartite motif family identifies cell compartments. EMBO J. 20, 2140\u20132151 (2001).","journal-title":"EMBO J."},{"key":"735_CR9","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1016\/S0092-8674(00)00077-5","volume":"102","author":"CA Joazeiro","year":"2000","unstructured":"Joazeiro, C. A. & Weissman, A. M. RING finger proteins: mediators of ubiquitin ligase activity. Cell 102, 549\u2013552 (2000).","journal-title":"Cell"},{"key":"735_CR10","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.16309","volume":"5","author":"JM Wagner","year":"2016","unstructured":"Wagner, J. M. et al. Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5alpha. Elife 5, e16309 (2016).","journal-title":"Elife"},{"key":"735_CR11","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1042\/BST20160325","volume":"45","author":"D Esposito","year":"2017","unstructured":"Esposito, D., Koliopoulos, M. G. & Rittinger, K. Structural determinants of TRIM protein function. Biochem. Soc. Trans. 45, 183\u2013191 (2017).","journal-title":"Biochem. Soc. Trans."},{"key":"735_CR12","doi-asserted-by":"publisher","first-page":"4369","DOI":"10.1128\/JVI.03172-15","volume":"90","author":"B Liu","year":"2016","unstructured":"Liu, B. et al. The C-Terminal Tail of TRIM56 dictates antiviral restriction of influenza A and B viruses by impeding viral RNA synthesis. J. Virol. 90, 4369\u20134382 (2016).","journal-title":"J. Virol."},{"key":"735_CR13","doi-asserted-by":"publisher","first-page":"105406","DOI":"10.1016\/j.antiviral.2022.105406","volume":"207","author":"X Tian","year":"2022","unstructured":"Tian, X. et al. TRIM56 impairs HBV infection and replication by inhibiting HBV core promoter activity. Antiviral Res. 207, 105406 (2022).","journal-title":"Antiviral Res."},{"key":"735_CR14","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1038\/nrc3139","volume":"11","author":"S Hatakeyama","year":"2011","unstructured":"Hatakeyama, S. TRIM proteins and cancer. Nat. Rev. Cancer 11, 792\u2013804 (2011).","journal-title":"Nat. Rev. Cancer"},{"key":"735_CR15","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.tibs.2017.01.002","volume":"42","author":"S Hatakeyama","year":"2017","unstructured":"Hatakeyama, S. TRIM family proteins: roles in autophagy, immunity, and carcinogenesis. Trends Biochem. Sci. 42, 297\u2013311 (2017).","journal-title":"Trends Biochem. Sci."},{"key":"735_CR16","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1126\/science.1232398","volume":"340","author":"I Barde","year":"2013","unstructured":"Barde, I. et al. A KRAB\/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science 340, 350\u2013353 (2013).","journal-title":"Science"},{"key":"735_CR17","doi-asserted-by":"publisher","first-page":"123","DOI":"10.4161\/auto.26841","volume":"10","author":"MM Khan","year":"2014","unstructured":"Khan, M. M. et al. Role of autophagy, SQSTM1, SH3GLB1, and TRIM63 in the turnover of nicotinic acetylcholine receptors. Autophagy 10, 123\u2013136 (2014).","journal-title":"Autophagy"},{"key":"735_CR18","doi-asserted-by":"publisher","first-page":"2378","DOI":"10.1016\/j.molimm.2010.05.004","volume":"47","author":"M Niida","year":"2010","unstructured":"Niida, M., Tanaka, M. & Kamitani, T. Downregulation of active IKK beta by Ro52-mediated autophagy. Mol. Immunol. 47, 2378\u20132387 (2010).","journal-title":"Mol. Immunol."},{"key":"735_CR19","doi-asserted-by":"publisher","first-page":"e76140","DOI":"10.1371\/journal.pone.0076140","volume":"8","author":"V Pizon","year":"2013","unstructured":"Pizon, V. et al. MURF2B, a novel LC3-binding protein, participates with MURF2A in the switch between autophagy and ubiquitin proteasome system during differentiation of C2C12 muscle cells. PLoS One 8, e76140 (2013).","journal-title":"PLoS One"},{"key":"735_CR20","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.chom.2009.04.006","volume":"5","author":"MU Gack","year":"2009","unstructured":"Gack, M. U. et al. Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Cell Host Microbe 5, 439\u2013449 (2009).","journal-title":"Cell Host Microbe"},{"key":"735_CR21","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.chom.2014.07.015","volume":"16","author":"M Laurent-Rolle","year":"2014","unstructured":"Laurent-Rolle, M. et al. The interferon signaling antagonist function of yellow fever virus NS5 protein is activated by type I interferon. Cell Host Microbe 16, 314\u2013327 (2014).","journal-title":"Cell Host Microbe"},{"key":"735_CR22","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1016\/j.cytogfr.2014.04.008","volume":"25","author":"G Maarifi","year":"2014","unstructured":"Maarifi, G., Chelbi-Alix, M. K. & Nisole, S. PML control of cytokine signaling. Cytokine Growth Factor Rev. 25, 551\u2013561 (2014).","journal-title":"Cytokine Growth Factor Rev."},{"key":"735_CR23","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/ni0404-355","volume":"5","author":"M Stevenson","year":"2004","unstructured":"Stevenson, M. TRIMming HIV-1\u2019s mainsail. Nat. Immunol. 5, 355\u2013356 (2004).","journal-title":"Nat. Immunol."},{"key":"735_CR24","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/s12929-017-0374-4","volume":"24","author":"P Czerwi\u0144ska","year":"2017","unstructured":"Czerwi\u0144ska, P., Mazurek, S. & Wiznerowicz, M. The complexity of TRIM28 contribution to cancer. J. Biomed. Sci. 24, 63 (2017).","journal-title":"J. Biomed. Sci."},{"key":"735_CR25","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1016\/j.acthis.2013.12.009","volume":"116","author":"Y Kanno","year":"2014","unstructured":"Kanno, Y. et al. TRIM29 as a novel prostate basal cell marker for diagnosis of prostate cancer. Acta Histochem. 116, 708\u2013712 (2014).","journal-title":"Acta Histochem."},{"key":"735_CR26","doi-asserted-by":"publisher","first-page":"1500","DOI":"10.1038\/ng.2007.15","volume":"39","author":"K Khetchoumian","year":"2007","unstructured":"Khetchoumian, K. et al. Loss of Trim24 (Tif1alpha) gene function confers oncogenic activity to retinoic acid receptor alpha. Nat. Genet. 39, 1500\u20131506 (2007).","journal-title":"Nat. Genet."},{"key":"735_CR27","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1016\/0014-4827(92)90068-J","volume":"202","author":"K Brasch","year":"1992","unstructured":"Brasch, K. & Ochs, R. L. Nuclear bodies (NBs): a newly \u201crediscovered\u201d organelle. Exp. Cell Res. 202, 211\u2013223 (1992).","journal-title":"Exp. Cell Res."},{"key":"735_CR28","first-page":"570","volume":"47","author":"M Riviere","year":"1960","unstructured":"Riviere, M. & Bernhard, W. J. B. C. Examen au microscope \u00e9lectronique de la tumeur VX2 du lapin domestique d\u00e9riv\u00e9e du papillome de Shope. Bull. Cancer 47, 570\u2013584 (1960).","journal-title":"Bull. Cancer"},{"key":"735_CR29","doi-asserted-by":"publisher","first-page":"51","DOI":"10.7150\/ijbs.6.51","volume":"6","author":"E Van Damme","year":"2010","unstructured":"Van Damme, E., Laukens, K., Dang, T. H. & Van Ostade, X. A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int. J. Biol. Sci. 6, 51\u201367 (2010).","journal-title":"Int. J. Biol. Sci."},{"key":"735_CR30","doi-asserted-by":"publisher","first-page":"6138","DOI":"10.1128\/MCB.20.16.6138-6146.2000","volume":"20","author":"DB Bloch","year":"2000","unstructured":"Bloch, D. B. et al. Sp110 localizes to the PML-Sp100 nuclear body and may function as a nuclear hormone receptor transcriptional coactivator. Mol. Cell. Biol. 20, 6138\u20136146 (2000).","journal-title":"Mol. Cell. Biol."},{"key":"735_CR31","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1016\/j.it.2020.04.007","volume":"41","author":"I Fraschilla","year":"2020","unstructured":"Fraschilla, I. & Jeffrey, K. L. The speckled protein (SP) family: immunity\u2019s chromatin readers. Trends Immunol. 41, 572\u2013585 (2020).","journal-title":"Trends Immunol."},{"key":"735_CR32","doi-asserted-by":"publisher","first-page":"26675","DOI":"10.1074\/jbc.273.41.26675","volume":"273","author":"T Kamitani","year":"1998","unstructured":"Kamitani, T. et al. Identification of three major sentrinization sites in PML. J. Biol. Chem. 273, 26675\u201326682 (1998).","journal-title":"J. Biol. Chem."},{"key":"735_CR33","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/j.molcel.2006.09.013","volume":"24","author":"TH Shen","year":"2006","unstructured":"Shen, T. H., Lin, H. K., Scaglioni, P. P., Yung, T. M. & Pandolfi, P. P. The mechanisms of PML-nuclear body formation. Mol. Cell 24, 331\u2013339 (2006).","journal-title":"Mol. Cell"},{"key":"735_CR34","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1016\/j.trecan.2020.05.005","volume":"6","author":"Y Li","year":"2020","unstructured":"Li, Y., Ma, X., Wu, W., Chen, Z. & Meng, G. PML nuclear body biogenesis, carcinogenesis, and targeted therapy. Trends Cancer 6, 889\u2013906 (2020).","journal-title":"Trends Cancer"},{"key":"735_CR35","doi-asserted-by":"publisher","first-page":"4549","DOI":"10.3390\/cancers14194549","volume":"14","author":"MC Liebl","year":"2022","unstructured":"Liebl, M. C. & Hofmann, T. G. Regulating the p53 tumor suppressor network at PML biomolecular condensates. Cancers 14, 4549 (2022).","journal-title":"Cancers"},{"key":"735_CR36","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.dnarep.2019.04.001","volume":"78","author":"M Vancurova","year":"2019","unstructured":"Vancurova, M. et al. PML nuclear bodies are recruited to persistent DNA damage lesions in an RNF168-53BP1 dependent manner and contribute to DNA repair. DNA Repair 78, 114\u2013127 (2019).","journal-title":"DNA Repair"},{"key":"735_CR37","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.1038\/sj.onc.1205227","volume":"21","author":"R Carbone","year":"2002","unstructured":"Carbone, R., Pearson, M., Minucci, S. & Pelicci, P. G. PML NBs associate with the hMre11 complex and p53 at sites of irradiation induced DNA damage. Oncogene 21, 1633\u20131640 (2002).","journal-title":"Oncogene"},{"key":"735_CR38","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1002\/bies.20089","volume":"26","author":"G Dellaire","year":"2004","unstructured":"Dellaire, G. & Bazett-Jones, D. P. PML nuclear bodies: dynamic sensors of DNA damage and cellular stress. Bioessays 26, 963\u2013977 (2004).","journal-title":"Bioessays"},{"key":"735_CR39","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.1038\/sj.onc.1206140","volume":"22","author":"H Seker","year":"2003","unstructured":"Seker, H. et al. UV-C-induced DNA damage leads to p53-dependent nuclear trafficking of PML. Oncogene 22, 1620\u201311628 (2003).","journal-title":"Oncogene"},{"key":"735_CR40","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/978-1-4614-5398-7_5","volume":"770","author":"F Cammas","year":"2012","unstructured":"Cammas, F., Khetchoumian, K., Chambon, P. & Losson, R. TRIM involvement in transcriptional regulation. Adv. Exp. Med. Biol. 770, 59\u201376 (2012).","journal-title":"Adv. Exp. Med. Biol."},{"key":"735_CR41","doi-asserted-by":"publisher","first-page":"5557","DOI":"10.1038\/sj.onc.1205666","volume":"21","author":"W Fang","year":"2002","unstructured":"Fang, W., Mori, T. & Cobrinik, D. Regulation of PML-dependent transcriptional repression by pRB and low penetrance pRB mutants. Oncogene 21, 5557\u20135565 (2002).","journal-title":"Oncogene"},{"key":"735_CR42","doi-asserted-by":"publisher","first-page":"E85","DOI":"10.1038\/35010583","volume":"2","author":"S Zhong","year":"2000","unstructured":"Zhong, S., Salomoni, P. & Pandolfi, P. P. The transcriptional role of PML and the nuclear body. Nat. Cell Biol. 2, E85\u2013E90 (2000).","journal-title":"Nat. Cell Biol."},{"key":"735_CR43","doi-asserted-by":"publisher","first-page":"1366","DOI":"10.1016\/j.stemcr.2017.03.006","volume":"8","author":"C Hadjimichael","year":"2017","unstructured":"Hadjimichael, C. et al. Promyelocytic leukemia protein is an essential regulator of stem cell pluripotency and somatic cell reprogramming. Stem Cell Rep. 8, 1366\u20131378 (2017).","journal-title":"Stem Cell Rep."},{"key":"735_CR44","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1038\/ncb1147","volume":"6","author":"R Bernardi","year":"2004","unstructured":"Bernardi, R. et al. PML regulates p53 stability by sequestering Mdm2 to the nucleolus. Nat. Cell Biol. 6, 665\u2013672 (2004).","journal-title":"Nat. Cell Biol."},{"key":"735_CR45","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1002\/1878-0261.12486","volume":"13","author":"N Sachini","year":"2019","unstructured":"Sachini, N. et al. Promyelocytic leukemia protein (PML) controls breast cancer cell proliferation by modulating Forkhead transcription factors. Mol. Oncol. 13, 1369\u20131387 (2019).","journal-title":"Mol. Oncol."},{"key":"735_CR46","doi-asserted-by":"publisher","first-page":"2475","DOI":"10.1158\/0008-5472.CAN-17-3091","volume":"78","author":"C Song","year":"2018","unstructured":"Song, C. et al. PML recruits TET2 to regulate DNA modification and cell proliferation in response to chemotherapeutic agent. Cancer Res. 78, 2475\u20132489 (2018).","journal-title":"Cancer Res."},{"key":"735_CR47","first-page":"1590","volume":"55","author":"B Terris","year":"1995","unstructured":"Terris, B. et al. PML nuclear bodies are general targets for inflammation and cell proliferation. Cancer Res. 55, 1590\u20131597 (1995).","journal-title":"Cancer Res."},{"key":"735_CR48","doi-asserted-by":"publisher","first-page":"6299","DOI":"10.1038\/onc.2008.305","volume":"27","author":"R Bernardi","year":"2008","unstructured":"Bernardi, R., Papa, A. & Pandolfi, P. P. Regulation of apoptosis by PML and the PML-NBs. Oncogene 27, 6299\u20136312 (2008).","journal-title":"Oncogene"},{"key":"735_CR49","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1038\/35036365","volume":"2","author":"A Guo","year":"2000","unstructured":"Guo, A. et al. The function of PML in p53-dependent apoptosis. Nat. Cell Biol. 2, 730\u2013736 (2000).","journal-title":"Nat. Cell Biol."},{"key":"735_CR50","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.607526","volume":"10","author":"M Collados Rodr\u00edguez","year":"2020","unstructured":"Collados Rodr\u00edguez, M. The fate of speckled protein 100 (Sp100) during herpesviruses infection. Front. Cell. Infect. Microbiol. 10, 607526 (2020).","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"735_CR51","doi-asserted-by":"publisher","first-page":"e0125690","DOI":"10.1371\/journal.pone.0125690","volume":"10","author":"F Giovannoni","year":"2015","unstructured":"Giovannoni, F., Damonte, E. B. & Garc\u00eda, C. C. Cellular promyelocytic leukemia protein is an important dengue virus restriction factor. PLoS One 10, e0125690 (2015).","journal-title":"PLoS One"},{"key":"735_CR52","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1093\/emboj\/17.1.61","volume":"17","author":"S M\u00fcller","year":"1998","unstructured":"M\u00fcller, S., Matunis, M. J. & Dejean, A. Conjugation with the ubiquitin-related modifier SUMO-1 regulates the partitioning of PML within the nucleus. EMBO J. 17, 61\u201370 (1998).","journal-title":"EMBO J."},{"key":"735_CR53","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1083\/jcb.201305148","volume":"204","author":"U Sahin","year":"2014","unstructured":"Sahin, U. et al. Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins. J. Cell Biol. 204, 931\u2013945 (2014).","journal-title":"J. Cell Biol."},{"key":"735_CR54","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.1038\/nrm2277","volume":"8","author":"R Bernardi","year":"2007","unstructured":"Bernardi, R. & Pandolfi, P. P. Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies. Nat. Rev. Mol. Cell Biol. 8, 1006\u20131016 (2007).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"735_CR55","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s13578-015-0051-9","volume":"5","author":"D Guan","year":"2015","unstructured":"Guan, D. & Kao, H. Y. The function, regulation and therapeutic implications of the tumor suppressor protein, PML. Cell Biosci. 5, 60 (2015).","journal-title":"Cell Biosci."},{"key":"735_CR56","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1038\/nm.2882","volume":"18","author":"K Ito","year":"2012","unstructured":"Ito, K. et al. A PML\u2013PPAR-\u03b4 pathway for fatty acid oxidation regulates hematopoietic stem cell maintenance. Nat. Med. 18, 1350\u20131358 (2012).","journal-title":"Nat. Med."},{"key":"735_CR57","doi-asserted-by":"publisher","first-page":"a000661","DOI":"10.1101\/cshperspect.a000661","volume":"2","author":"V Lallemand-Breitenbach","year":"2010","unstructured":"Lallemand-Breitenbach, V. & de Th\u00e9, H. PML nuclear bodies. Cold Spring Harb. Perspect. Biol. 2, a000661 (2010).","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"735_CR58","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nrmicro1248","volume":"3","author":"S Nisole","year":"2005","unstructured":"Nisole, S., Stoye, J. P. & Sa\u00efb, A. TRIM family proteins: retroviral restriction and antiviral defence. Nat. Rev. Microbiol. 3, 799\u2013808 (2005).","journal-title":"Nat. Rev. Microbiol."},{"key":"735_CR59","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1002\/path.2126","volume":"211","author":"A Varadaraj","year":"2007","unstructured":"Varadaraj, A. et al. Evidence for the receipt of DNA damage stimuli by PML nuclear domains. J. Pathol. 211, 471\u2013480 (2007).","journal-title":"J. Pathol."},{"key":"735_CR60","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11746-0","volume":"10","author":"Y Li","year":"2019","unstructured":"Li, Y. et al. B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis. Nat. Commun. 10, 3789 (2019).","journal-title":"Nat. Commun."},{"key":"735_CR61","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03498-0","volume":"9","author":"P Wang","year":"2018","unstructured":"Wang, P. et al. RING tetramerization is required for nuclear body biogenesis and PML sumoylation. Nat. Commun. 9, 1277 (2018).","journal-title":"Nat. Commun."},{"key":"735_CR62","doi-asserted-by":"publisher","DOI":"10.1096\/fj.202300216R","volume":"37","author":"W Wu","year":"2023","unstructured":"Wu, W. et al. Phase separation is required for PML nuclear body biogenesis and function. FASEB J. 37, e22986 (2023).","journal-title":"FASEB J."},{"key":"735_CR63","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1038\/nmeth.4347","volume":"14","author":"YZ Tan","year":"2017","unstructured":"Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793\u2013796 (2017).","journal-title":"Nat. Methods"},{"key":"735_CR64","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44577-1","volume":"15","author":"X Meng","year":"2024","unstructured":"Meng, X. et al. Multi-scale structures of the mammalian radial spoke and divergence of axonemal complexes in ependymal cilia. Nat. Commun. 15, 362 (2024).","journal-title":"Nat. Commun."},{"key":"735_CR65","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2021180118","volume":"118","author":"W Zheng","year":"2021","unstructured":"Zheng, W. et al. Distinct architecture and composition of mouse axonemal radial spoke head revealed by cryo-EM. Proc. Natl. Acad. Sci. USA 118, e2021180118 (2021).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"735_CR66","doi-asserted-by":"publisher","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","volume":"50","author":"M Varadi","year":"2022","unstructured":"Varadi, M. et al. AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439\u2013D444 (2022).","journal-title":"Nucleic Acids Res."},{"key":"735_CR67","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583\u2013589 (2021).","journal-title":"Nature"},{"key":"735_CR68","doi-asserted-by":"publisher","first-page":"2548","DOI":"10.1158\/2159-8290.CD-23-0453","volume":"13","author":"P Bercier","year":"2023","unstructured":"Bercier, P. et al. Structural basis of PML-RARA oncoprotein targeting by arsenic unravels a cysteine rheostat controlling PML body assembly and function. Cancer Discov. 13, 2548\u20132565 (2023).","journal-title":"Cancer Discov."},{"key":"735_CR69","doi-asserted-by":"publisher","first-page":"2601","DOI":"10.1016\/j.molcel.2024.05.031","volume":"84","author":"HJ Kim","year":"2024","unstructured":"Kim, H. J. et al. Structure of the Hir histone chaperone complex. Mol. Cell 84, 2601\u20132617 (2024).","journal-title":"Mol. Cell"},{"key":"735_CR70","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1002\/pro.2458","volume":"23","author":"ED Merkley","year":"2014","unstructured":"Merkley, E. D. et al. Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Sci. 23, 747\u2013759 (2014).","journal-title":"Protein Sci."},{"key":"735_CR71","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.1038\/s41594-023-01111-7","volume":"30","author":"SH Park","year":"2023","unstructured":"Park, S. H. et al. Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane. Nat. Struct. Mol. Biol. 30, 1695\u20131706 (2023).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"735_CR72","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.1016\/j.str.2019.05.003","volume":"27","author":"M Lim","year":"2019","unstructured":"Lim, M. et al. A ubiquitin-binding domain that binds a structural fold distinct from that of ubiquitin. Structure 27, 1316\u20131325.e6 (2019).","journal-title":"Structure"},{"key":"735_CR73","doi-asserted-by":"publisher","first-page":"15042","DOI":"10.1073\/pnas.1901318116","volume":"116","author":"GA Stoll","year":"2019","unstructured":"Stoll, G. A. et al. Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing. Proc. Natl. Acad. Sci. USA 116, 15042\u201315051 (2019).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"735_CR74","doi-asserted-by":"publisher","first-page":"3197","DOI":"10.1084\/jem.20160301","volume":"214","author":"M Niwa-Kawakita","year":"2017","unstructured":"Niwa-Kawakita, M. et al. PML is a ROS sensor activating p53 upon oxidative stress. J. Exp. Med. 214, 3197\u20133206 (2017).","journal-title":"J. Exp. Med."},{"key":"735_CR75","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.str.2015.10.024","volume":"24","author":"S Nie","year":"2016","unstructured":"Nie, S. et al. Coiled-Coil domains of SUN proteins as intrinsic dynamic regulators. Structure 24, 80\u201391 (2016).","journal-title":"Structure"},{"key":"735_CR76","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.202306142","volume":"223","author":"MU Rios","year":"2024","unstructured":"Rios, M. U. et al. Multivalent coiled-coil interactions enable full-scale centrosome assembly and strength. J. Cell Biol. 223, e202306142 (2024).","journal-title":"J. Cell Biol."},{"key":"735_CR77","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1002\/bies.201600062","volume":"38","author":"L Truebestein","year":"2016","unstructured":"Truebestein, L. & Leonard, T. A. Coiled-coils: the long and short of it. Bioessays 38, 903\u20139916 (2016).","journal-title":"Bioessays"},{"key":"735_CR78","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1111\/jipb.13032","volume":"63","author":"J Wang","year":"2021","unstructured":"Wang, J., Han, M. & Liu, Y. Diversity, structure and function of the coiled-coil domains of plant NLR immune receptors. J. Integr. Plant Biol. 63, 283\u2013296 (2021).","journal-title":"J. Integr. Plant Biol."},{"key":"735_CR79","doi-asserted-by":"crossref","unstructured":"Cohen, C. et al. Promyelocytic leukemia (PML) nuclear bodies (NBs) induce latent\/quiescent HSV-1 genomes chromatinization through a PML NB\/Histone H3.3\/H3.3 Chaperone Axis. PLoS Pathog. 14, e1007313 (2018).","DOI":"10.1371\/journal.ppat.1007313"},{"key":"735_CR80","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1038\/347558a0","volume":"347","author":"H de Th\u00e9","year":"1990","unstructured":"de Th\u00e9, H., Chomienne, C., Lanotte, M., Degos, L. & Dejean, A. The t(15;17) translocation of acute promyelocytic leukaemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus. Nature 347, 558\u2013561 (1990).","journal-title":"Nature"},{"key":"735_CR81","doi-asserted-by":"crossref","unstructured":"Gentric, G. et al. PML-regulated mitochondrial metabolism enhances chemosensitivity in human ovarian cancers. Cell Metab. 29, 156\u2013173.e10 (2019).","DOI":"10.1016\/j.cmet.2018.09.002"},{"key":"735_CR82","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1016\/j.tranon.2019.05.010","volume":"12","author":"P Gong","year":"2019","unstructured":"Gong, P. et al. Telomere maintenance-associated PML is a potential specific therapeutic target of human colorectal cancer. Transl. Oncol. 12, 1164\u20131176 (2019).","journal-title":"Transl. Oncol."},{"key":"735_CR83","doi-asserted-by":"publisher","first-page":"4339","DOI":"10.1073\/pnas.1217602110","volume":"110","author":"A Iwanami","year":"2013","unstructured":"Iwanami, A. et al. PML mediates glioblastoma resistance to mammalian target of rapamycin (mTOR)-targeted therapies. Proc. Natl. Acad. Sci. USA 110, 4339\u20134344 (2013).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"735_CR84","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1016\/j.bbrc.2012.11.108","volume":"430","author":"M Kuroki","year":"2013","unstructured":"Kuroki, M. et al. PML tumor suppressor protein is required for HCV production. Biochem. Biophys. Res. Commun. 430, 592\u20135597 (2013).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"735_CR85","doi-asserted-by":"publisher","first-page":"12447","DOI":"10.1096\/fj.201901091R","volume":"33","author":"M Swayden","year":"2019","unstructured":"Swayden, M. et al. PML hyposumoylation is responsible for the resistance of pancreatic cancer. FASEB J. 33, 12447\u201312463 (2019).","journal-title":"FASEB J."},{"key":"735_CR86","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/s11010-017-3081-2","volume":"436","author":"B Yang","year":"2017","unstructured":"Yang, B., Yao, J., Li, B., Shao, G. & Cui, Y. Inhibition of protein kinase CK2 sensitizes non-small cell lung cancer cells to cisplatin via upregulation of PML. Mol. Cell. Biochem. 436, 87\u201397 (2017).","journal-title":"Mol. Cell. Biochem."},{"key":"735_CR87","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1002\/(SICI)1097-0215(20000301)85:5<599::AID-IJC1>3.0.CO;2-#","volume":"85","author":"P Zhang","year":"2000","unstructured":"Zhang, P. et al. Lack of expression for the suppressor PML in human small cell lung carcinoma. Int. J. Cancer 85, 599\u2013605 (2000).","journal-title":"Int. J. Cancer"},{"key":"735_CR88","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33147-6","volume":"13","author":"S Tessier","year":"2022","unstructured":"Tessier, S. et al. Exploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells. Nat. Commun. 13, 5726 (2022).","journal-title":"Nat. Commun."},{"key":"735_CR89","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1016\/j.devcel.2006.10.011","volume":"11","author":"MJ Matunis","year":"2006","unstructured":"Matunis, M. J., Zhang, X. D. & Ellis, N. A. SUMO: the glue that binds. Dev. Cell 11, 596\u2013597 (2006).","journal-title":"Dev. Cell"},{"key":"735_CR90","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/nmeth.3283","volume":"12","author":"S Lu","year":"2015","unstructured":"Lu, S. et al. Mapping native disulfide bonds at a proteome scale. Nat. Methods 12, 329\u2013331 (2015).","journal-title":"Nat. Methods"},{"key":"735_CR91","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/nmeth.2099","volume":"9","author":"B Yang","year":"2012","unstructured":"Yang, B. et al. Identification of cross-linked peptides from complex samples. Nat. Methods 9, 904\u2013906 (2012).","journal-title":"Nat. Methods"},{"key":"735_CR92","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00476-w","volume":"8","author":"WF Wang","year":"2017","unstructured":"Wang, W. F. et al. HSP70-Hrd1 axis precludes the oncorepressor potential of N-terminal misfolded Blimp-1s in lymphoma cells. Nat. Commun. 8, 363 (2017).","journal-title":"Nat. Commun."},{"key":"735_CR93","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1038\/nmeth.4193","volume":"14","author":"SQ Zheng","year":"2017","unstructured":"Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331\u2013332 (2017).","journal-title":"Nat. Methods"},{"key":"735_CR94","doi-asserted-by":"publisher","first-page":"4169","DOI":"10.1042\/BCJ20210708","volume":"478","author":"D Kimanius","year":"2021","unstructured":"Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem. J. 478, 4169\u20134185 (2021).","journal-title":"Biochem. J."},{"key":"735_CR95","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1016\/j.jsb.2015.08.008","volume":"192","author":"A Rohou","year":"2015","unstructured":"Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216\u20132221 (2015).","journal-title":"J. Struct. Biol."},{"key":"735_CR96","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.jsb.2018.11.012","volume":"205","author":"M Su","year":"2019","unstructured":"Su, M. goCTF: Geometrically optimized CTF determination for single-particle cryo-EM. J. Struct. Biol. 205, 22\u201329 (2019).","journal-title":"J. Struct. Biol."},{"key":"735_CR97","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nmeth.4169","volume":"14","author":"A Punjani","year":"2017","unstructured":"Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290\u2013296 (2017).","journal-title":"Nat. Methods"},{"key":"735_CR98","doi-asserted-by":"publisher","first-page":"874","DOI":"10.1038\/s42003-021-02399-1","volume":"4","author":"R Sanchez-Garcia","year":"2021","unstructured":"Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).","journal-title":"Commun. Biol."},{"key":"735_CR99","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen, E. F. et al. UCSF Chimera\u2013a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"735_CR100","doi-asserted-by":"publisher","first-page":"3031","DOI":"10.1021\/acs.jctc.7b00125","volume":"13","author":"RF Alford","year":"2017","unstructured":"Alford, R. F. et al. The rosetta all-atom energy function for macromolecular modeling and design. J. Chem. Theory Comput. 13, 3031\u20133048 (2017).","journal-title":"J. Chem. Theory Comput."},{"key":"735_CR101","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1107\/S0907444910007493","volume":"66","author":"P Emsley","year":"2010","unstructured":"Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486\u2013501 (2010).","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"735_CR102","doi-asserted-by":"crossref","unstructured":"Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519\u2013530 (2018).","DOI":"10.1107\/S2059798318002425"},{"key":"735_CR103","doi-asserted-by":"crossref","unstructured":"Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531\u2013544 (2018).","DOI":"10.1107\/S2059798318006551"},{"key":"735_CR104","doi-asserted-by":"crossref","unstructured":"Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861\u2013877 (2019).","DOI":"10.1107\/S2059798319011471"},{"key":"735_CR105","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1002\/pro.3943","volume":"30","author":"EF Pettersen","year":"2021","unstructured":"Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70\u201382 (2021).","journal-title":"Protein Sci."},{"key":"735_CR106","doi-asserted-by":"publisher","first-page":"959160","DOI":"10.3389\/fbinf.2022.959160","volume":"2","author":"I Johansson-\u00c5khe","year":"2022","unstructured":"Johansson-\u00c5khe, I. & Wallner, B. Improving peptide-protein docking with AlphaFold-Multimer using forced sampling. Front. Bioinform. 2, 959160 (2022).","journal-title":"Front. Bioinform."}],"container-title":["Cell Discovery"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41421-024-00735-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41421-024-00735-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41421-024-00735-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,25]],"date-time":"2024-11-25T13:02:23Z","timestamp":1732539743000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41421-024-00735-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,25]]},"references-count":106,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["735"],"URL":"https:\/\/doi.org\/10.1038\/s41421-024-00735-3","relation":{},"ISSN":["2056-5968"],"issn-type":[{"value":"2056-5968","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,25]]},"assertion":[{"value":"3 April 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 September 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"118"}}