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Harold and Leila Y. Mathers Foundation","doi-asserted-by":"publisher","award":["MF-2112-02288"],"award-info":[{"award-number":["MF-2112-02288"]}],"id":[{"id":"10.13039\/100011671","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000738","name":"U.S. Department of Veterans Affairs","doi-asserted-by":"publisher","award":["I01BX000446"],"award-info":[{"award-number":["I01BX000446"]}],"id":[{"id":"10.13039\/100000738","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2026,5,5]]},"abstract":"<jats:p>\n                    Hypoxia inducible factors (HIFs) are heterodimeric transcription factors that coordinate cellular responses to low oxygen levels by binding a short hypoxia response element (HRE) DNA sequence near O\n                    <jats:sub>2<\/jats:sub>\n                    -regulated genes. Prior studies suggest HIF\/HRE complexes are augmented by the binding of additional factors nearby, but those interactions are not well understood. Here, we integrated structural and biochemical approaches to investigate several functionally relevant HIF assemblies with other protein, small molecule, and DNA partners. First, we used cryo\u2013electron microscopy (cryo-EM) to establish that HIF-1 and HIF-2 self-assemble into \u201cdimer-of-heterodimers\u201d (DoHD) complexes on extended human EPO enhancer sequences, with one heterodimer bound at a canonical HRE site and the second binding in an inverted fashion to an HRE-adjacent sequence 8 bp away. Consistent with ARNT PAS-B domains predominating interactions within a DoHD, we found HIF-1 and HIF-2 coassemble mixed DoHD complexes on the same DNA. Second, we saw that despite the increased complexities of the larger complexes, ligands for the isolated ARNT or HIF-2\u03b1 PAS-B domains still bound and disrupted both heterodimeric and DoHD complexes, albeit with variable potencies depending on the ligand. Finally, we combined cryo-EM and hydrogen\u2013deuterium exchange by mass spectrometry (HDX-MS) to show how HIF-1 and HIF-2 heterodimers engage the transforming acidic coiled-coil containing protein 3 coactivator via both ARNT and HIF-\u03b1 subunits, though this was unseen in the larger DoHD. Our findings highlight the importance of molecular context in biomolecular complex formation, adding to the complexities of potential regulation.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2514042123","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T17:59:57Z","timestamp":1777399197000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":0,"title":["Context-dependent variability of HIF heterodimers influences interactions with macromolecular and small molecule partners"],"prefix":"10.1073","volume":"123","author":[{"given":"Joseph D.","family":"Closson","sequence":"first","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]},{"name":"Ph.D. Program in Biochemistry, The Graduate Center\u2013City University of New York","place":["New York"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9609-4755","authenticated-orcid":false,"given":"Xingjian","family":"Xu","sequence":"additional","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]},{"name":"Ph.D. Program in Biochemistry, The Graduate Center\u2013City University of New York","place":["New York"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0670-6018","authenticated-orcid":false,"given":"Meiling","family":"Zhang","sequence":"additional","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tarsisius T.","family":"Tiyani","sequence":"additional","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]},{"name":"Ph.D. Program in Biochemistry, The Graduate Center\u2013City University of New York","place":["New York"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6067-0725","authenticated-orcid":false,"given":"Leandro Pimentel","family":"Marcelino","sequence":"additional","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]},{"name":"Department of Chemistry and Biochemistry, City College of New York","place":["New York"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6242-9297","authenticated-orcid":false,"given":"Eta A.","family":"Isiorho","sequence":"additional","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4507-6581","authenticated-orcid":false,"given":"Jason S.","family":"Nagati","sequence":"additional","affiliation":[{"name":"Department of Medicine, Columbia University Irving Medical Center","place":["New York"]},{"name":"Department of Medicine, James J. Peters Veterans Affairs Medical Center","place":["Bronx"]},{"name":"Department of Research & Development, James J. Peters Veterans Affairs Medical Center","place":["Bronx"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5621-7538","authenticated-orcid":false,"given":"Joseph A.","family":"Garcia","sequence":"additional","affiliation":[{"name":"Department of Medicine, Columbia University Irving Medical Center","place":["New York"]},{"name":"Department of Medicine, James J. Peters Veterans Affairs Medical Center","place":["Bronx"]},{"name":"Department of Research & Development, James J. Peters Veterans Affairs Medical Center","place":["Bronx"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8671-2556","authenticated-orcid":false,"given":"Kevin H.","family":"Gardner","sequence":"additional","affiliation":[{"name":"Structural Biology Initiative, City University of New York Advanced Science Research Center","place":["New York"]},{"name":"Department of Chemistry and Biochemistry, City College of New York","place":["New York"]},{"name":"Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center\u2013City University of New York","place":["New 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heterodimers contribute to ccRCC","author":"Mello R. 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Rastinejad, NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors. Elife 5, e18790 (2016).","journal-title":"Elife"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56574-7"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(03)00450-7"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl361"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.1007\/s13277-015-3810-7"},{"key":"e_1_3_5_58_2","doi-asserted-by":"publisher","DOI":"10.1186\/s10020-021-00298-z"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.22067"},{"key":"e_1_3_5_60_2","doi-asserted-by":"crossref","unstructured":"E. A. Isiorho X. Xu K. H. Gardner C-terminal coiled coil dimer of human TACC3. RCSB Worldwide Protein Data Bank. https:\/\/www.rcsb.org\/structure\/9YDY. 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