{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:23Z","timestamp":1792790303144,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,2]]},"group-title":"Biophysics","reference-count":46,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ARPA-H","award":["1AY1AX000035"],"award-info":[{"award-number":["1AY1AX000035"]}]},{"award":["GM143805"],"award-info":[{"award-number":["GM143805"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["DRG-2558-25"],"award-info":[{"award-number":["DRG-2558-25"]}],"id":[{"id":"https:\/\/ror.org\/01gd7b947","id-type":"ROR","asserted-by":"publisher"}]},{"name":"German Research Foundation","award":["556478029"],"award-info":[{"award-number":["556478029"]}],"id":[{"id":"https:\/\/ror.org\/018mejw64","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Cytochrome P450 3A4 (CYP3A4) metabolizes roughly half of all marketed drugs, and its inhibition can cause clinically significant drug-drug interactions. The enzyme accommodates chemically diverse ligands, making binding modes and metabolic outcomes difficult to predict. Previous X-ray crystallography efforts have leveraged a truncated construct without the N-terminal segment that tethers CYP3A4 to the membrane. Here we show that the same construct assembles into a symmetric trimer that can be resolved by cryo-EM and determine structures of both unliganded and ligand-bound CYP3A4. Multiple ligands are resolved with density consistent with several mutually exclusive conformations. Protein remodeling to reshape the binding pocket is concentrated in the F\/G loop, which is poorly resolved and unmodeled in many X-ray structures. These features likely underlie the poor predictive performance of co-folding methods on this target. The routine use of cryo-EM to resolve CYP3A4 ligand-bound complexes will provide the ground truth data needed to make predictive models of drug metabolism useful in practice.<\/jats:p>","DOI":"10.64898\/2026.09.01.748687","type":"posted-content","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T07:25:21Z","timestamp":1788420321000},"source":"Crossref","is-referenced-by-count":0,"title":["Structural Plasticity and Ligand Promiscuity of CYP3A4 Revealed by Cryo-EM"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8526-0383","authenticated-orcid":false,"given":"Anna Karen","family":"Orta","sequence":"first","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8163-1629","authenticated-orcid":false,"given":"Jan-Hannes","family":"Sch\u00e4fer","sequence":"additional","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA"},{"name":"Department of Chemistry, Chi-Huey Wong Laboratories for Biomedical Research, Scripps Research, La Jolla, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5155-7325","authenticated-orcid":false,"given":"Galen J.","family":"Correy","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7524-3310","authenticated-orcid":false,"given":"Jordan O.","family":"Norman","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3153-1256","authenticated-orcid":false,"given":"Julius","family":"Pampel","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3019-901X","authenticated-orcid":false,"given":"Kate K.","family":"Huddleston","sequence":"additional","affiliation":[{"name":"OpenADMET, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7393-7457","authenticated-orcid":false,"given":"Hugo","family":"MacDermott-Opeskin","sequence":"additional","affiliation":[{"name":"OpenADMET, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1590-5788","authenticated-orcid":false,"given":"Edward B.","family":"Miller","sequence":"additional","affiliation":[{"name":"Schr\u00f6dinger, Inc., New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2311-2155","authenticated-orcid":false,"given":"Gabriella","family":"Reggiano","sequence":"additional","affiliation":[{"name":"Schr\u00f6dinger, Inc., New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9796-3193","authenticated-orcid":false,"given":"Jo\u00e3o P. 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