{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T07:01:01Z","timestamp":1791874861191,"version":"4.3.4"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T00:00:00Z","timestamp":1558310400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T00:00:00Z","timestamp":1558310400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Struct Mol Biol"],"published-print":{"date-parts":[[2019,6]]},"DOI":"10.1038\/s41594-019-0220-3","type":"journal-article","created":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T12:03:42Z","timestamp":1558353822000},"page":"397-406","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":86,"title":["Transcription preinitiation complex structure and dynamics provide insight into genetic diseases"],"prefix":"10.1038","volume":"26","author":[{"given":"Chunli","family":"Yan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3149-013X","authenticated-orcid":false,"given":"Thomas","family":"Dodd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1659-2429","authenticated-orcid":false,"given":"John A.","family":"Tainer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan E.","family":"Tsutakawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5306-1005","authenticated-orcid":false,"given":"Ivaylo","family":"Ivanov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,5,20]]},"reference":[{"key":"220_CR1","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.cell.2009.02.001","volume":"136","author":"MJ Moore","year":"2009","unstructured":"Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688\u2013700 (2009).","journal-title":"Cell"},{"key":"220_CR2","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1016\/S0092-8674(02)00617-7","volume":"108","author":"NJ Proudfoot","year":"2002","unstructured":"Proudfoot, N. J., Furger, A. & Dye, M. J. Integrating rnRNA processing with transcription. Cell 108, 501\u2013512 (2002).","journal-title":"Cell"},{"key":"220_CR3","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1038\/nrg3662","volume":"15","author":"DL Bentley","year":"2014","unstructured":"Bentley, D. L. Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163\u2013175 (2014).","journal-title":"Nat. Rev. Genet."},{"key":"220_CR4","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0968-0004(96)10050-5","volume":"21","author":"RG Roeder","year":"1996","unstructured":"Roeder, R. G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21, 327\u2013335 (1996).","journal-title":"Trends Biochem. Sci."},{"key":"220_CR5","doi-asserted-by":"publisher","first-page":"2258","DOI":"10.7150\/jca.16966","volume":"7","author":"M Zurita","year":"2016","unstructured":"Zurita, M. & Cruz-Becerra, G. TFIIH: new discoveries regarding its mechanisms and impact on cancer treatment. J. Cancer 7, 2258\u20132265 (2016).","journal-title":"J. Cancer"},{"key":"220_CR6","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.3390\/molecules23051123","volume":"23","author":"A Hishikawa","year":"2018","unstructured":"Hishikawa, A., Hayashi, K. & Itoh, H. Transcription factors as therapeutic targets in chronic kidney disease. Molecules 23, 1123\u20131136 (2018).","journal-title":"Molecules"},{"key":"220_CR7","first-page":"571","volume":"134","author":"J Villard","year":"2004","unstructured":"Villard, J. Transcription regulation and human diseases. Swiss Med. Wkly 134, 571\u2013579 (2004).","journal-title":"Swiss Med. Wkly"},{"key":"220_CR8","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/1756-6606-6-44","volume":"6","author":"XF Chen","year":"2013","unstructured":"Chen, X. F., Zhang, Y. W., Xu, H. X. & Bu, G. J. Transcriptional regulation and its misregulation in Alzheimer\u2019s disease. Mol. Brain 6, 44\u201353 (2013).","journal-title":"Mol. Brain"},{"key":"220_CR9","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1016\/j.cell.2013.02.014","volume":"152","author":"TI Lee","year":"2013","unstructured":"Lee, T. I. & Young, R. A. Transcriptional regulation and its misregulation in disease. Cell 152, 1237\u20131251 (2013).","journal-title":"Cell"},{"key":"220_CR10","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1016\/S0092-8674(00)81061-2","volume":"84","author":"JA Goodrich","year":"1996","unstructured":"Goodrich, J. A., Cutler, G. & Tjian, R. Contacts in context: promoter specificity and macromolecular interactions in transcription. Cell 84, 825\u2013830 (1996).","journal-title":"Cell"},{"key":"220_CR11","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1016\/j.febslet.2004.11.027","volume":"579","author":"H Boeger","year":"2005","unstructured":"Boeger, H. et al. Structural basis of eukaryotic gene transcription. FEBS Lett. 579, 899\u2013903 (2005).","journal-title":"FEBS Lett."},{"key":"220_CR12","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1016\/0092-8674(89)90578-3","volume":"56","author":"S Buratowski","year":"1989","unstructured":"Buratowski, S., Hahn, S., Guarente, L. & Sharp, P. A. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56, 549\u2013561 (1989).","journal-title":"Cell"},{"key":"220_CR13","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1126\/science.1206629","volume":"333","author":"X Liu","year":"2011","unstructured":"Liu, X., Bushnell, D. A., Silva, D. A., Huang, X. H. & Kornberg, R. D. Initiation complex structure and promoter proofreading. Science 333, 633\u2013637 (2011).","journal-title":"Science"},{"key":"220_CR14","doi-asserted-by":"publisher","first-page":"4755","DOI":"10.1038\/emboj.2011.396","volume":"30","author":"ACM Cheung","year":"2011","unstructured":"Cheung, A. C. M., Sainsbury, S. & Cramer, P. Structural basis of initial RNA polymerase II transcription. Embo J. 30, 4755\u20134763 (2011).","journal-title":"Embo J."},{"key":"220_CR15","doi-asserted-by":"publisher","first-page":"2437","DOI":"10.1101\/gad.1235904","volume":"18","author":"RJ Sim","year":"2004","unstructured":"Sim, R. J., Belotserkovskaya, R. & Reinberg, D. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437\u20132468 (2004).","journal-title":"Genes Dev."},{"key":"220_CR16","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/nature17970","volume":"533","author":"Y He","year":"2016","unstructured":"He, Y. et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533, 359\u2013365 (2016).","journal-title":"Nature"},{"key":"220_CR17","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nature24282","volume":"551","author":"S Schilbach","year":"2017","unstructured":"Schilbach, S. et al. Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature 551, 204\u2013209 (2017).","journal-title":"Nature"},{"key":"220_CR18","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1038\/nature11991","volume":"495","author":"Y He","year":"2013","unstructured":"He, Y., Fang, J., Taatjes, D. J. & Nogales, E. Structural visualization of key steps in human transcription initiation. Nature 495, 481\u2013486 (2013).","journal-title":"Nature"},{"key":"220_CR19","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1038\/nature23903","volume":"549","author":"BJ Greber","year":"2017","unstructured":"Greber, B. J. et al. The cryo-electron microscopy structure of human transcription factor IIH. Nature 549, 414\u2013417 (2017).","journal-title":"Nature"},{"key":"220_CR20","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1016\/S1097-2765(03)00182-5","volume":"11","author":"S Dubaele","year":"2003","unstructured":"Dubaele, S. et al. Basal transcription defect discriminates between xeroderma pigmentosum and trichothiodystrophy in XPD patients. Mol. Cell 11, 1635\u20131646 (2003).","journal-title":"Mol. Cell"},{"key":"220_CR21","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1101\/sqb.1998.63.105","volume":"63","author":"F Coin","year":"1998","unstructured":"Coin, F. & Egly, J. M. Ten years of TFIIH. Cold Spring Harb. Symp. Quant. Biol. 63, 105\u2013110 (1998).","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"220_CR22","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1101\/gad.859501","volume":"15","author":"AR Lehmann","year":"2001","unstructured":"Lehmann, A. R. The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseases. Genes Dev. 15, 15\u201323 (2001).","journal-title":"Genes Dev."},{"key":"220_CR23","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/S0065-2660(01)43004-5","volume":"43","author":"M Berneburg","year":"2001","unstructured":"Berneburg, M. & Lehmann, A. R. Xeroderma pigmentosum and related disorders: defects in DNA repair and transcription. Adv. Genet. 43, 71\u2013102 (2001).","journal-title":"Adv. Genet."},{"key":"220_CR24","doi-asserted-by":"publisher","first-page":"E1236","DOI":"10.1073\/pnas.1519444113","volume":"113","author":"H Fassihi","year":"2016","unstructured":"Fassihi, H. et al. Deep phenotyping of 89 xeroderma pigmentosum patients reveals unexpected heterogeneity dependent on the precise molecular defect. Proc. Natl Acad. Sci. USA 113, E1236\u2013E1245 (2016).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"220_CR25","doi-asserted-by":"publisher","first-page":"1194","DOI":"10.1002\/humu.20768","volume":"29","author":"J Boyle","year":"2008","unstructured":"Boyle, J. et al. Persistence of repair proteins at unrepaired DNA damage distinguishes diseases with ERCC2 (XPD) mutations: cancer-prone xeroderma pigmentosum vs. non-cancer-prone trichothiodystrophy. Hum. Mutat. 29, 1194\u20131208 (2008).","journal-title":"Hum. Mutat."},{"key":"220_CR26","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1002\/pro.3424","volume":"27","author":"JK Rimel","year":"2018","unstructured":"Rimel, J. K. & Taatjes, D. J. The essential and multifunctional TFIIH complex. Protein Sci. 27, 1018\u20131037 (2018).","journal-title":"Protein Sci."},{"key":"220_CR27","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1146\/annurev-biochem-060815-014857","volume":"85","author":"E Compe","year":"2016","unstructured":"Compe, E. & Egly, J. M. Nucleotide excision repair and transcriptional regulation: TFIIH and Beyond. Annu. Rev. Biochem. 85, 265\u2013290 (2016).","journal-title":"Annu. Rev. Biochem."},{"key":"220_CR28","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.ajhg.2014.12.012","volume":"96","author":"A Singh","year":"2015","unstructured":"Singh, A., Compe, E., Le May, N. & Egly, J. M. TFIIH subunit alterations causing xeroderma pigmentosum and trichothiodystrophy specifically disturb several steps during transcription. Am. J. Hum. Genet. 96, 194\u2013207 (2015).","journal-title":"Am. J. Hum. Genet."},{"key":"220_CR29","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/nrm3350","volume":"13","author":"E Compe","year":"2012","unstructured":"Compe, E. & Egly, J. M. TFIIH: when transcription met DNA repair. Nat. Rev. Mol. Cell Biol. 13, 343\u2013354 (2012).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"220_CR30","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/j.tibs.2013.09.002","volume":"38","author":"S Grunberg","year":"2013","unstructured":"Grunberg, S. & Hahn, S. Structural insights into transcription initiation by RNA polymerase II. Trends Biochem. Sci. 38, 603\u2013611 (2013).","journal-title":"Trends Biochem. Sci."},{"key":"220_CR31","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/nsmb.2334","volume":"19","author":"S Grunberg","year":"2012","unstructured":"Grunberg, S., Warfield, L. & Hahn, S. Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nat. Struct. Mol. Biol. 19, 788\u2013796 (2012).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"220_CR32","doi-asserted-by":"publisher","first-page":"3961","DOI":"10.1073\/pnas.1417709112","volume":"112","author":"J Fishburn","year":"2015","unstructured":"Fishburn, J., Tomko, E., Galburt, E. & Hahn, S. Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation. Proc. Natl Acad. Sci. USA 112, 3961\u20133966 (2015).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"220_CR33","doi-asserted-by":"publisher","first-page":"e16105","DOI":"10.7554\/eLife.16105","volume":"5","author":"A Singharoy","year":"2016","unstructured":"Singharoy, A. et al. Molecular dynamics-based model refinement and validation for sub-5 angstrom cryo-electron microscopy maps. eLlife 5, e16105 (2016).","journal-title":"eLlife"},{"key":"220_CR34","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1016\/j.molcel.2015.07.016","volume":"59","author":"J Luo","year":"2015","unstructured":"Luo, J. et al. Architecture of the human and yeast general transcription and DNA repair factor TFIIH. Mol. Cell 59, 794\u2013806 (2015).","journal-title":"Mol. Cell"},{"key":"220_CR35","doi-asserted-by":"publisher","first-page":"942","DOI":"10.1016\/j.dnarep.2012.09.003","volume":"11","author":"QZ Zhu","year":"2012","unstructured":"Zhu, Q. Z., Wani, G., Sharma, N. & Wani, A. Lack of CAK complex accumulation at DNA damage sites in XP-B and XP-B\/CS fibroblasts reveals differential regulation of CAK anchoring to core TFIIH by XPB and XPD helicases during nucleotide excision repair. DNA Repair 11, 942\u2013950 (2012).","journal-title":"DNA Repair"},{"key":"220_CR36","doi-asserted-by":"publisher","first-page":"6488","DOI":"10.1073\/pnas.93.13.6488","volume":"93","author":"R Drapkin","year":"1996","unstructured":"Drapkin, R., LeRoy, G., Cho, H., Akoulitchev, S. & Reinberg, D. Human cyclin-dependent kinase-activating kinase exists in three distinct complexes. Proc. Natl Acad. Sci. USA 93, 6488\u20136493 (1996).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"220_CR37","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1016\/j.dnarep.2011.04.028","volume":"10","author":"JO Fuss","year":"2011","unstructured":"Fuss, J. O. & Tainer, J. A. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair 10, 697\u2013713 (2011).","journal-title":"DNA Repair"},{"key":"220_CR38","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.molcel.2007.03.009","volume":"26","author":"F Coin","year":"2007","unstructured":"Coin, F., Oksenych, V. & Egly, J. M. Distinct roles for the XPB\/p52 and XPD\/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair. Mol. Cell 26, 245\u2013256 (2007).","journal-title":"Mol. Cell"},{"key":"220_CR39","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2008.04.030","volume":"133","author":"L Fan","year":"2008","unstructured":"Fan, L. et al. XPD helicase structures and activities: Insights into the cancer and aging phenotypes from XPD mutations. Cell 133, 789\u2013800 (2008).","journal-title":"Cell"},{"key":"220_CR40","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.pbiomolbio.2014.12.005","volume":"117","author":"L Fan","year":"2015","unstructured":"Fan, L. & DuPrez, K. T. XPB: an unconventional SF2 DNA helicase. Prog. Biophys. Mol. Biol. 117, 174\u2013181 (2015).","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"220_CR41","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.molcel.2006.02.017","volume":"22","author":"L Fan","year":"2006","unstructured":"Fan, L. et al. Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol. Cell 22, 27\u201337 (2006).","journal-title":"Mol. Cell"},{"key":"220_CR42","doi-asserted-by":"publisher","first-page":"E633","DOI":"10.1073\/pnas.1213981110","volume":"110","author":"W Abdulrahman","year":"2013","unstructured":"Abdulrahman, W. et al. ARCH domain of XPD, an anchoring platform for CAK that conditions TFIIH DNA repair and transcription activities. Proc. Natl Acad. Sci. USA 110, E633\u2013E642 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"220_CR43","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1038\/35037509","volume":"407","author":"G Obmolova","year":"2000","unstructured":"Obmolova, G., Ban, C., Hsieh, P. & Yang, W. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407, 703\u2013710 (2000).","journal-title":"Nature"},{"key":"220_CR44","doi-asserted-by":"publisher","first-page":"7618","DOI":"10.1073\/pnas.1324143111","volume":"111","author":"AC Mason","year":"2014","unstructured":"Mason, A. C. et al. A structure-specific nucleic acid-binding domain conserved among DNA repair proteins. Proc. Natl Acad. Sci. USA 111, 7618\u20137623 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"220_CR45","doi-asserted-by":"publisher","first-page":"e42400","DOI":"10.7554\/eLife.42400","volume":"7","author":"K Cheng","year":"2018","unstructured":"Cheng, K. & Wigley, D. B. DNA translocation mechanism of an XPD family helicase. eLife 7, e42400 (2018).","journal-title":"eLife"},{"key":"220_CR46","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1038\/emboj.2008.47","volume":"27","author":"M Okuda","year":"2008","unstructured":"Okuda, M. et al. Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. Embo J. 27, 1161\u20131171 (2008).","journal-title":"Embo J."},{"key":"220_CR47","doi-asserted-by":"publisher","first-page":"4856","DOI":"10.1128\/MCB.15.9.4856","volume":"15","author":"Y Ohkuma","year":"1995","unstructured":"Ohkuma, Y., Hashimoto, S., Wang, C. K., Horikoshi, M. & Roeder, R. G. Analysis of the role of TFIIE in basal transcription and TFIIH-mediated carboxy-terminal domain phosphorylation through structure-function studies of TFIIE-alpha. Mol. Cell. Biol. 15, 4856\u20134866 (1995).","journal-title":"Mol. Cell. Biol."},{"key":"220_CR48","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/978-1-62703-658-0_11","volume":"1084","author":"CC David","year":"2014","unstructured":"David, C. C. & Jacobs, D. J. Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol. Biol. 1084, 193\u2013226 (2014).","journal-title":"Methods Mol. Biol."},{"key":"220_CR49","doi-asserted-by":"publisher","first-page":"3000","DOI":"10.1093\/bioinformatics\/bts546","volume":"28","author":"J Eargle","year":"2012","unstructured":"Eargle, J. & Luthey-Schulten, Z. NetworkView: 3D display and analysis of protein center dot RNA interaction networks. Bioinformatics 28, 3000\u20133001 (2012).","journal-title":"Bioinformatics"},{"key":"220_CR50","doi-asserted-by":"crossref","first-page":"18414","DOI":"10.1016\/S0021-9258(17)32324-4","volume":"269","author":"JD Parvin","year":"1994","unstructured":"Parvin, J. D., Shykind, B. M., Meyers, R. E., Kim, J. S. & Sharp, P. A. Multiple sets of basal factors initiate transcription by RNA-Polymerase-II. J. Biol. Chem. 269, 18414\u201318421 (1994).","journal-title":"J. Biol. Chem."},{"key":"220_CR51","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1016\/0092-8674(93)90140-L","volume":"73","author":"JD Parvin","year":"1993","unstructured":"Parvin, J. D. & Sharp, P. A. DNA topology and a minimal set of basal factors for transcription by RNA Polymerase-II. Cell 73, 533\u2013540 (1993).","journal-title":"Cell"},{"key":"220_CR52","doi-asserted-by":"publisher","first-page":"3031","DOI":"10.1084\/jem.20091892","volume":"206","author":"T Ueda","year":"2009","unstructured":"Ueda, T. et al. alleles contribute to the phenotype of compound heterozygote xeroderma pigmentosum patients. J. Exp. Med. 206, 3031\u20133046 (2009).","journal-title":"J. Exp. Med."},{"key":"220_CR53","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/jid.2011.426","volume":"132","author":"JJ DiGiovanna","year":"2012","unstructured":"DiGiovanna, J. J. & Kraemer, K. H. Shining a light on xeroderma pigmentosum. J. Invest. Dermatol. 132, 785\u2013796 (2012).","journal-title":"J. Invest. Dermatol."},{"key":"220_CR54","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1016\/j.ajhg.2016.02.008","volume":"98","author":"C Kuschal","year":"2016","unstructured":"Kuschal, C. et al. GTF2E2 mutations destabilize the general transcription factor complex TFIIE in individuals with DNA repair-proficient trichothiodystrophy. Am. J. Hum. Genet. 98, 627\u2013642 (2016).","journal-title":"Am. J. Hum. Genet."},{"key":"220_CR55","doi-asserted-by":"publisher","first-page":"e44771","DOI":"10.7554\/eLife.44771","volume":"8","author":"BJ Greber","year":"2019","unstructured":"Greber, B. J., Toso, D. B., Fang, J. & Nogales, E. The complete structure of the human TFIIH core complex. eLife 8, e44771 (2019).","journal-title":"eLife"},{"key":"220_CR56","doi-asserted-by":"publisher","first-page":"3305","DOI":"10.1093\/nar\/gkg557","volume":"31","author":"MA Kurowski","year":"2003","unstructured":"Kurowski, M. A. & Bujnicki, J. M. GeneSilico protein structure prediction meta-server. Nucleic Acids Res. 31, 3305\u20133307 (2003).","journal-title":"Nucleic Acids Res."},{"key":"220_CR57","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.1107\/S0907444904019158","volume":"60","author":"P Emsley","year":"2004","unstructured":"Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126\u20132132 (2004).","journal-title":"Acta Crystallogr. D"},{"key":"220_CR58","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","volume":"234","author":"A Sali","year":"1993","unstructured":"Sali, A. & Blundell, T. L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779\u2013815 (1993).","journal-title":"J. Mol. Biol."},{"key":"220_CR59","doi-asserted-by":"publisher","first-page":"10872","DOI":"10.1093\/nar\/gkx743","volume":"45","author":"L Radu","year":"2017","unstructured":"Radu, L. et al. The intricate network between the p34 and p44 subunits is central to the activity of the transcription\/DNA repair factor TFIIH. Nucleic Acids Res. 45, 10872\u201310883 (2017).","journal-title":"Nucleic Acids Res."},{"key":"220_CR60","doi-asserted-by":"publisher","first-page":"7457","DOI":"10.1074\/jbc.M007963200","volume":"276","author":"V Gervais","year":"2001","unstructured":"Gervais, V. et al. Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit - New insights into the RING finger family. J. Biol. Chem. 276, 7457\u20137464 (2001).","journal-title":"J. Biol. Chem."},{"key":"220_CR61","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 - a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"220_CR62","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/j.str.2008.03.005","volume":"16","author":"LG Trabuco","year":"2008","unstructured":"Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673\u2013683 (2008).","journal-title":"Structure"},{"key":"220_CR63","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1107\/S0907444909052925","volume":"66","author":"PD Adams","year":"2010","unstructured":"Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213\u2013221 (2010).","journal-title":"Acta Crystallogr. D"},{"key":"220_CR64","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1107\/S2059798318006551","volume":"74","author":"PV Afonine","year":"2018","unstructured":"Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531\u2013544 (2018).","journal-title":"Acta Crystallogr. D"},{"key":"220_CR65","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"DA Case","year":"2005","unstructured":"Case, D. A. et al. The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668\u20131688 (2005).","journal-title":"J. Comput. Chem."},{"key":"220_CR66","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926\u2013935 (1983).","journal-title":"J. Chem. Phys."},{"key":"220_CR67","doi-asserted-by":"publisher","first-page":"1990","DOI":"10.1063\/1.463137","volume":"97","author":"M Tuckerman","year":"1992","unstructured":"Tuckerman, M., Berne, B. J. & Martyna, G. J. Reversible multiple time scale molecular-dynamics. J. Chem. Phys. 97, 1990\u20132001 (1992).","journal-title":"J. Chem. Phys."},{"key":"220_CR68","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1006\/jcph.1999.6201","volume":"151","author":"L Kale","year":"1999","unstructured":"Kale, L. et al. NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 151, 283\u2013312 (1999).","journal-title":"J. Comput. Phys."},{"key":"220_CR69","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"JC Phillips","year":"2005","unstructured":"Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781\u20131802 (2005).","journal-title":"J. Comput. Chem."},{"key":"220_CR70","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"JA Maier","year":"2015","unstructured":"Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696\u20133713 (2015).","journal-title":"J. Chem. Theory Comput."},{"key":"220_CR71","doi-asserted-by":"publisher","first-page":"W68","DOI":"10.1093\/nar\/gkr316","volume":"39","author":"C Blanchet","year":"2011","unstructured":"Blanchet, C., Pasi, M., Zakrzewska, K. & Lavery, R. CURVES plus web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures. Nucleic Acids Res. 39, W68\u2013W73 (2011).","journal-title":"Nucleic Acids Res."},{"key":"220_CR72","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1002\/prot.340170408","volume":"17","author":"A Amadei","year":"1993","unstructured":"Amadei, A., Linssen, A. B. & Berendsen, H. J. Essential dynamics of proteins. Proteins 17, 412\u2013425 (1993).","journal-title":"Proteins"},{"key":"220_CR73","doi-asserted-by":"publisher","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"DR Roe","year":"2013","unstructured":"Roe, D. R. & Cheatham, T. E. 3rd PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084\u20133095 (2013).","journal-title":"J. Chem. Theory Comput."},{"key":"220_CR74","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 27\u201328 (1996).","journal-title":"J. Mol. Graph."},{"key":"220_CR75","doi-asserted-by":"publisher","first-page":"1765","DOI":"10.1002\/jcc.20482","volume":"27","author":"NM Glykos","year":"2006","unstructured":"Glykos, N. M. Software news and updates. Carma: a molecular dynamics analysis program. J. Comput. Chem. 27, 1765\u20131768 (2006).","journal-title":"J. Comput. Chem."}],"container-title":["Nature Structural & Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/s41594-019-0220-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41594-019-0220-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41594-019-0220-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T18:23:53Z","timestamp":1684607033000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41594-019-0220-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,20]]},"references-count":75,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2019,6]]}},"alternative-id":["220"],"URL":"https:\/\/doi.org\/10.1038\/s41594-019-0220-3","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.735802305.793571138","asserted-by":"object"}]},"ISSN":["1545-9993","1545-9985"],"issn-type":[{"value":"1545-9993","type":"print"},{"value":"1545-9985","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,20]]},"assertion":[{"value":"20 December 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 May 2019","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":"Competing interests"}}]}}