{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T00:32:29Z","timestamp":1793061149181,"version":"4.5.0"},"reference-count":74,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T00:00:00Z","timestamp":1793491200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T00:00:00Z","timestamp":1793491200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["RR190046"],"award-info":[{"award-number":["RR190046"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["35GM142722"],"award-info":[{"award-number":["35GM142722"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["jbc.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biological Chemistry"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1016\/j.jbc.2026.113611","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T23:10:36Z","timestamp":1790723436000},"page":"113611","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cryo-EM structures reveal upstream DNA interactions within the mitochondrial transcription initiation complex"],"prefix":"10.1016","volume":"302","author":[{"given":"Rory E.","family":"Sharkey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caitlin","family":"Schroeder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangyu","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jamie","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0903-8932","authenticated-orcid":false,"given":"Alfredo J.","family":"Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4037-0431","authenticated-orcid":false,"given":"Yang","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jbc.2026.113611_bib1","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature14156","article-title":"Mitochondrial DNA stress primes the antiviral innate immune response","volume":"520","author":"West","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.113611_bib2","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1007\/s10495-007-0756-2","article-title":"Mitochondria, oxidative stress and cell death","volume":"12","author":"Ott","year":"2007","journal-title":"Apoptosis"},{"key":"10.1016\/j.jbc.2026.113611_bib3","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/290457a0","article-title":"Sequence and organization of the human mitochondrial genome","volume":"290","author":"Anderson","year":"1981","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.113611_bib4","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/S0005-2728(98)00161-3","article-title":"The mitochondrial genome: structure, transcription, translation and replication","volume":"1410","author":"Taanman","year":"1999","journal-title":"Biochim. Biophys. Acta (Bba) - Bioenerg."},{"key":"10.1016\/j.jbc.2026.113611_bib5","doi-asserted-by":"crossref","first-page":"11122","DOI":"10.1073\/pnas.0805399105","article-title":"Human mitochondrial RNA polymerase primes lagging-strand DNA synthesis in vitro","volume":"105","author":"Wanrooij","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.113611_bib6","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/s41467-023-36277-7","article-title":"TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease","volume":"14","author":"Van Haute","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.113611_bib7","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/s41420-024-01926-3","article-title":"Mitochondria transcription and cancer","volume":"10","author":"Lei","year":"2024","journal-title":"Cell Death Discov"},{"key":"10.1016\/j.jbc.2026.113611_bib8","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1038\/s41467-021-21279-0","article-title":"POLRMT mutations impair mitochondrial transcription causing neurological disease","volume":"12","author":"Ol\u00e1hov\u00e1","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.113611_bib9","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.1600963","article-title":"POLRMT regulates the switch between replication primer formation and gene expression of Mammalian mtDNA","volume":"2","author":"K\u00fchl","year":"2016","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jbc.2026.113611_bib10","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.tibs.2013.09.002","article-title":"Structural insights into transcription initiation by RNA polymerase II","volume":"38","author":"Gr\u00fcnberg","year":"2013","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.jbc.2026.113611_bib11","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/s41580-023-00661-4","article-title":"Mechanisms and regulation of human mitochondrial transcription","volume":"25","author":"Tan","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol"},{"key":"10.1016\/j.jbc.2026.113611_bib12","doi-asserted-by":"crossref","first-page":"16083","DOI":"10.1016\/S0021-9258(19)85387-5","article-title":"Mitochondrial transcription initiation. Variation and conservation","volume":"268","author":"Shadel","year":"1993","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib13","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/nature10435","article-title":"Structure of human mitochondrial RNA polymerase","volume":"478","author":"Ringel","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.113611_bib14","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/nsmb.2159","article-title":"The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA","volume":"18","author":"Ngo","year":"2011","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.113611_bib15","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1016\/j.cell.2017.10.036","article-title":"Structural basis of mitochondrial transcription initiation","volume":"171","author":"Hillen","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib16","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/0092-8674(87)90220-0","article-title":"Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements","volume":"50","author":"Fisher","year":"1987","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib17","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1016\/j.cell.2009.10.031","article-title":"TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase","volume":"139","author":"Sologub","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib18","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1074\/jbc.M116.751008","article-title":"Human mitochondrial transcription factor B2 is required for promoter melting during initiation of transcription","volume":"292","author":"Posse","year":"2017","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib19","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1093\/nar\/gkw1157","article-title":"Human mitochondrial transcription factors TFAM and TFB2M work synergistically in promoter melting during transcription initiation","volume":"45","author":"Ramachandran","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib20","doi-asserted-by":"crossref","first-page":"3646","DOI":"10.1016\/j.molcel.2022.08.011","article-title":"The human mitochondrial genome contains a second light strand promoter","volume":"82","author":"Tan","year":"2022","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib21","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.110000","article-title":"The TFAM-to-mtDNA ratio defines inner-cellular nucleoid populations with distinct activity levels","volume":"37","author":"Br\u00fcser","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jbc.2026.113611_bib22","doi-asserted-by":"crossref","first-page":"2309","DOI":"10.1016\/j.cell.2022.05.006","article-title":"Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization","volume":"185","author":"Zhu","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib23","doi-asserted-by":"crossref","first-page":"3137","DOI":"10.1016\/j.molcel.2025.07.002","article-title":"Human mitochondrial RNA polymerase structures reveal transcription start site and slippage mechanism","volume":"85","author":"Shen","year":"2025","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib24","doi-asserted-by":"crossref","first-page":"3123","DOI":"10.1016\/j.molcel.2025.06.016","article-title":"Structural basis for promoter recognition and transcription factor binding and release in human mitochondria","volume":"85","author":"Herbine","year":"2025","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib25","doi-asserted-by":"crossref","first-page":"3638","DOI":"10.1093\/nar\/gkt1397","article-title":"The amino terminal extension of mammalian mitochondrial RNA polymerase ensures promoter specific transcription initiation","volume":"42","author":"Posse","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib26","doi-asserted-by":"crossref","first-page":"4606","DOI":"10.1038\/sj.emboj.7600465","article-title":"The mitochondrial RNA polymerase contributes critically to promoter specificity in mammalian cells","volume":"23","author":"Gaspari","year":"2004","journal-title":"EMBO J."},{"key":"10.1016\/j.jbc.2026.113611_bib27","doi-asserted-by":"crossref","first-page":"3884","DOI":"10.1093\/nar\/gkt1356","article-title":"A novel intermediate in transcription initiation by human mitochondrial RNA polymerase","volume":"42","author":"Morozov","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib28","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.27283","article-title":"Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter","volume":"6","author":"Uchida","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.jbc.2026.113611_bib29","doi-asserted-by":"crossref","first-page":"13432","DOI":"10.1074\/jbc.C116.727966","article-title":"Human mitochondrial transcription initiation complexes have similar topology on the light and heavy strand promoters","volume":"291","author":"Morozov","year":"2016","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib30","doi-asserted-by":"crossref","first-page":"12133","DOI":"10.1073\/pnas.0910581107","article-title":"Core human mitochondrial transcription apparatus is a regulated two-component system in vitro","volume":"107","author":"Shutt","year":"2010","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.jbc.2026.113611_bib31","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/s41556-022-00887-y","article-title":"The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster","volume":"24","author":"Liu","year":"2022","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.jbc.2026.113611_bib32","doi-asserted-by":"crossref","first-page":"18145","DOI":"10.1074\/jbc.M117.797480","article-title":"Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases","volume":"292","author":"Sultana","year":"2017","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib33","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1038\/nsmb.2683","article-title":"Structure of human mitochondrial RNA polymerase elongation complex","volume":"20","author":"Schwinghammer","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.113611_bib34","doi-asserted-by":"crossref","first-page":"1640","DOI":"10.1093\/nar\/gkg251","article-title":"Human mitochondrial DNA is packaged with TFAM","volume":"31","author":"Istiaq Alam","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib35","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/nar\/gkr787","article-title":"Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA","volume":"40","author":"Malarkey","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib36","doi-asserted-by":"crossref","first-page":"2386","DOI":"10.1016\/j.bpj.2017.11.3743","article-title":"Protein flexibility and synergy of HMG domains underlie U-Turn bending of DNA by TFAM in solution","volume":"114","author":"Rubio-Cosials","year":"2018","journal-title":"Biophysical J."},{"key":"10.1016\/j.jbc.2026.113611_bib37","doi-asserted-by":"crossref","first-page":"17957","DOI":"10.1073\/pnas.1109594108","article-title":"Frustration in protein\u2013DNA binding influences conformational switching and target search kinetics","volume":"108","author":"Marcovitz","year":"2011","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.jbc.2026.113611_bib38","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1073\/pnas.1016020107","article-title":"A single-molecule characterization of p53 search on DNA","volume":"108","author":"Tafvizi","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.113611_bib39","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1128\/MMBR.63.2.457-478.1999","article-title":"DNA bending and wrapping around RNA polymerase: a \u201cRevolutionary\u201d model describing transcriptional mechanisms","volume":"63","author":"Coulombe","year":"1999","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.jbc.2026.113611_bib40","doi-asserted-by":"crossref","first-page":"9147","DOI":"10.1093\/nar\/16.19.9147","article-title":"RNA polymerase induces DNA bending at yeast mitochondria] promoters","volume":"16","author":"Schinkel","year":"1988","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib41","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1038\/ng.258","article-title":"The mitochondrial DNA genetic bottleneck results from replication of a subpopulation of genomes","volume":"40","author":"Wai","year":"2008","journal-title":"Nat. Genet."},{"key":"10.1016\/j.jbc.2026.113611_bib42","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1016\/j.molcel.2023.01.011","article-title":"Structural basis of a transcription pre-initiation complex on a divergent promoter","volume":"83","author":"Gorbea Col\u00f3n","year":"2023","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib43","doi-asserted-by":"crossref","first-page":"D445","DOI":"10.1093\/nar\/gkac998","article-title":"OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity","volume":"51","author":"Kuznetsov","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib44","doi-asserted-by":"crossref","first-page":"16109","DOI":"10.1074\/jbc.M111.228023","article-title":"The N-terminal domain of the yeast mitochondrial RNA polymerase regulates multiple steps of transcription","volume":"286","author":"Paratkar","year":"2011","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib45","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1038\/s41586-023-06643-y","article-title":"Structures illustrate step-by-step mitochondrial transcription initiation","volume":"622","author":"Goovaerts","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.113611_bib46","doi-asserted-by":"crossref","first-page":"12785","DOI":"10.1016\/S0021-9258(18)45275-1","article-title":"Specificity factor of yeast mitochondrial RNA polymerase. Purification and interaction with core RNA polymerase","volume":"262","author":"Schinkel","year":"1987","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib47","doi-asserted-by":"crossref","first-page":"2762","DOI":"10.1105\/tpc.109.068536","article-title":"Phage-type RNA polymerase RPOTmp performs gene-specific transcription in Mitochondria of Arabidopsis thaliana","volume":"21","author":"K\u00fchn","year":"2009","journal-title":"Plant Cell"},{"key":"10.1016\/j.jbc.2026.113611_bib48","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1093\/genetics\/148.4.1763","article-title":"Functions of the high mobility group protein, Abf2p, in mitochondrial DNA segregation, recombination and copy number in Saccharomyces cerevisiae","volume":"148","author":"Zelenaya-Troitskaya","year":"1998","journal-title":"Genetics"},{"key":"10.1016\/j.jbc.2026.113611_bib49","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s12964-016-0132-3","article-title":"The new (dis)order in RNA regulation","volume":"14","author":"J\u00e4rvelin","year":"2016","journal-title":"Cell Commun Signal"},{"key":"10.1016\/j.jbc.2026.113611_bib50","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1002\/pro.5560060106","article-title":"Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect","volume":"6","author":"Tsai","year":"1997","journal-title":"Protein Sci."},{"key":"10.1016\/j.jbc.2026.113611_bib51","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/S0959-440X(00)00065-8","article-title":"Electrostatic aspects of protein\u2013protein interactions","volume":"10","author":"Sheinerman","year":"2000","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/j.jbc.2026.113611_bib52","doi-asserted-by":"crossref","first-page":"5428","DOI":"10.1073\/pnas.90.12.5428","article-title":"A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions","volume":"90","author":"Wong","year":"1993","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.113611_bib53","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.57264","article-title":"How to measure and evaluate binding affinities","volume":"9","author":"Jarmoskaite","year":"2020","journal-title":"eLife"},{"key":"10.1016\/j.jbc.2026.113611_bib54","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1017\/S1431927603445911","article-title":"SerialEM: a program for automated tilt series acquisition on tecnai microscopes using prediction of specimen position","volume":"9","author":"Mastronarde","year":"2003","journal-title":"Microanal"},{"key":"10.1016\/j.jbc.2026.113611_bib55","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nmeth.4193","article-title":"MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy","volume":"14","author":"Zheng","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jbc.2026.113611_bib56","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jsb.2015.11.003","article-title":"Gctf: real-time CTF determination and correction","volume":"193","author":"Zhang","year":"2016","journal-title":"J. Struct. Biol."},{"key":"10.1016\/j.jbc.2026.113611_bib57","doi-asserted-by":"crossref","first-page":"4169","DOI":"10.1042\/BCJ20210708","article-title":"New tools for automated cryo-EM single-particle analysis in RELION-4.0","volume":"478","author":"Kimanius","year":"2021","journal-title":"Biochem. J."},{"key":"10.1016\/j.jbc.2026.113611_bib58","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1107\/S2052252520000081","article-title":"Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1","volume":"7","author":"Zivanov","year":"2020","journal-title":"IUCrJ"},{"key":"10.1016\/j.jbc.2026.113611_bib59","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/s41592-023-01853-8","article-title":"3DFlex: determining structure and motion of flexible proteins from cryo-EM","volume":"20","author":"Punjani","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jbc.2026.113611_bib60","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1038\/s41592-019-0575-8","article-title":"Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs","volume":"16","author":"Bepler","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jbc.2026.113611_bib61","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1107\/S2059798318004655","article-title":"Automated map sharpening by maximization of detail and connectivity","volume":"74","author":"Terwilliger","year":"2018","journal-title":"Acta Crystallogr. D Struct. Biol."},{"key":"10.1016\/j.jbc.2026.113611_bib62","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.jbc.2026.113611_bib63","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.113611_bib64","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Cryst. D"},{"key":"10.1016\/j.jbc.2026.113611_bib65","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: a comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2026.113611_bib66","doi-asserted-by":"crossref","first-page":"D444","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: the protein sequence classification resource in 2025","volume":"53","author":"Blum","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib67","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jbc.2026.113611_bib68","doi-asserted-by":"crossref","first-page":"W272","DOI":"10.1093\/nar\/gkag373","article-title":"HMMER web server: 2026 update","volume":"54","author":"Rajkovi\u0107","year":"2026","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib69","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jbc.2026.113611_bib70","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jbc.2026.113611_bib71","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib72","doi-asserted-by":"crossref","first-page":"W521","DOI":"10.1093\/nar\/gkae241","article-title":"The EMBL-EBI job dispatcher sequence analysis tools framework in 2024","volume":"52","author":"Madeira","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.113611_bib73","doi-asserted-by":"crossref","first-page":"3744","DOI":"10.1093\/bioinformatics\/btab491","article-title":"Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework","volume":"37","author":"Moffat","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jbc.2026.113611_bib74","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: a 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng."}],"container-title":["Journal of Biological Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S002192582602483X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S002192582602483X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T23:45:58Z","timestamp":1793058358000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S002192582602483X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,11]]},"references-count":74,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["S002192582602483X"],"URL":"https:\/\/doi.org\/10.1016\/j.jbc.2026.113611","relation":{},"ISSN":["0021-9258"],"issn-type":[{"value":"0021-9258","type":"print"}],"subject":[],"published":{"date-parts":[[2026,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Cryo-EM structures reveal upstream DNA interactions within the mitochondrial transcription initiation complex","name":"articletitle","label":"Article Title"},{"value":"Journal of Biological Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jbc.2026.113611","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}],"article-number":"113611"}}