{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T21:49:38Z","timestamp":1787003378201,"version":"build-2736575974"},"reference-count":77,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T00:00:00Z","timestamp":1676246400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T00:00:00Z","timestamp":1676246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Struct Mol Biol"],"published-print":{"date-parts":[[2023,3]]},"DOI":"10.1038\/s41594-022-00918-0","type":"journal-article","created":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T12:05:49Z","timestamp":1676289949000},"page":"296-308","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13"],"prefix":"10.1038","volume":"30","author":[{"given":"Sun Kyung","family":"Kim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miles Sasha","family":"Dickinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet","family":"Finer-Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8082-3423","authenticated-orcid":false,"given":"Ziqiang","family":"Guan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8341-3067","authenticated-orcid":false,"given":"Robyn M.","family":"Kaake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacia","family":"Echeverria","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jen","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3616-9743","authenticated-orcid":false,"given":"Ernst H.","family":"Pulido","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0435-6197","authenticated-orcid":false,"given":"Andrej","family":"Sali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4902-337X","authenticated-orcid":false,"given":"Nevan J.","family":"Krogan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5736-4388","authenticated-orcid":false,"given":"Oren S.","family":"Rosenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2083-5665","authenticated-orcid":false,"given":"Robert M.","family":"Stroud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,2,13]]},"reference":[{"key":"918_CR1","unstructured":"Global Tuberculosis Report 2021 (World Health Organization, 2021)."},{"key":"918_CR2","doi-asserted-by":"publisher","first-page":"5672","DOI":"10.1128\/JB.01919-07","volume":"190","author":"B Zuber","year":"2008","unstructured":"Zuber, B. et al. Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state. J. Bacteriol. 190, 5672\u20135680 (2008).","journal-title":"J. Bacteriol."},{"key":"918_CR3","doi-asserted-by":"publisher","first-page":"3963","DOI":"10.1073\/pnas.0709530105","volume":"105","author":"C Hoffmann","year":"2008","unstructured":"Hoffmann, C., Leis, A., Niederweis, M., Plitzko, J. M. & Engelhardt, H. Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure. Proc. Natl Acad. Sci. USA 105, 3963\u20133967 (2008).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"918_CR4","doi-asserted-by":"publisher","first-page":"e1000794","DOI":"10.1371\/journal.ppat.1000794","volume":"6","author":"M Sani","year":"2010","unstructured":"Sani, M. et al. Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins. PLoS Pathog. 6, e1000794 (2010).","journal-title":"PLoS Pathog."},{"key":"918_CR5","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1038\/nchembio.794","volume":"8","author":"AE Grzegorzewicz","year":"2012","unstructured":"Grzegorzewicz, A. E. et al. Inhibition of mycolic acid transport across the Mycobacterium tuberculosis plasma membrane. Nat. Chem. Biol. 8, 334\u2013341 (2012).","journal-title":"Nat. Chem. Biol."},{"key":"918_CR6","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/S2213-2600(19)30418-7","volume":"8","author":"E Harding","year":"2020","unstructured":"Harding, E. WHO global progress report on tuberculosis elimination. Lancet Respir. Med. 8, 19 (2020).","journal-title":"Lancet Respir. Med."},{"key":"918_CR7","doi-asserted-by":"publisher","first-page":"e75245","DOI":"10.1371\/journal.pone.0075245","volume":"8","author":"TR Ioerger","year":"2013","unstructured":"Ioerger, T. R. et al. Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS ONE 8, e75245 (2013).","journal-title":"PLoS ONE"},{"key":"918_CR8","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/nrmicro1816","volume":"6","author":"JC Sacchettini","year":"2008","unstructured":"Sacchettini, J. C., Rubin, E. J. & Freundlich, J. S. Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat. Rev. Microbiol. 6, 41\u201352 (2008).","journal-title":"Nat. Rev. Microbiol."},{"key":"918_CR9","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1073\/pnas.0305439101","volume":"101","author":"D Portevin","year":"2004","unstructured":"Portevin, D. et al. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proc. Natl Acad. Sci. USA 101, 314\u2013319 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"918_CR10","doi-asserted-by":"publisher","first-page":"19255","DOI":"10.1074\/jbc.M109.006940","volume":"284","author":"S Gavalda","year":"2009","unstructured":"Gavalda, S. et al. The Pks13\/FadD32 crosstalk for the biosynthesis of mycolic acids in Mycobacterium tuberculosis. J. Biol. Chem. 284, 19255\u201319264 (2009).","journal-title":"J. Biol. Chem."},{"key":"918_CR11","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1038\/nature02384","volume":"428","author":"OA Trivedi","year":"2004","unstructured":"Trivedi, O. A. et al. Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. Nature 428, 441\u2013445 (2004).","journal-title":"Nature"},{"key":"918_CR12","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1016\/j.chembiol.2009.03.012","volume":"16","author":"M L\u00e9ger","year":"2009","unstructured":"L\u00e9ger, M. et al. The dual function of the Mycobacterium tuberculosis FadD32 required for mycolic acid biosynthesis. Chem. Biol. 16, 510\u2013519 (2009).","journal-title":"Chem. Biol."},{"key":"918_CR13","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.chembiol.2013.11.011","volume":"21","author":"H Marrakchi","year":"2014","unstructured":"Marrakchi, H., Lan\u00e9elle, M.-A. & Daff\u00e9, M. Mycolic acids: structures, biosynthesis, and beyond. Chem. Biol. 21, 67\u201385 (2014).","journal-title":"Chem. Biol."},{"key":"918_CR14","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1038\/s41589-018-0026-3","volume":"14","author":"DA Herbst","year":"2018","unstructured":"Herbst, D. A. et al. The structural organization of substrate loading in iterative polyketide synthases. Nat. Chem. Biol. 14, 474\u2013479 (2018).","journal-title":"Nat. Chem. Biol."},{"key":"918_CR15","doi-asserted-by":"publisher","first-page":"E3243","DOI":"10.1073\/pnas.1402158111","volume":"111","author":"X Meniche","year":"2014","unstructured":"Meniche, X. et al. Subpolar addition of new cell wall is directed by DivIVA in mycobacteria. Proc. Natl Acad. Sci. USA 111, E3243\u2013E3251 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"918_CR16","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1002\/ijch.201800098","volume":"59","author":"C Khosla","year":"2019","unstructured":"Khosla, C. From active sites to machines: a challenge for enzyme chemists. Isr. J. Chem. 59, 37\u201340 (2019).","journal-title":"Isr. J. Chem."},{"key":"918_CR17","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1016\/j.cell.2017.06.025","volume":"170","author":"A Aggarwal","year":"2017","unstructured":"Aggarwal, A. et al. Development of a novel lead that targets M. tuberculosis polyketide synthase 13. Cell 170, 249\u2013259.e25 (2017).","journal-title":"Cell"},{"key":"918_CR18","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1016\/S0969-2126(02)00889-4","volume":"10","author":"H Pan","year":"2002","unstructured":"Pan, H. et al. Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway. Structure 10, 1559\u20131568 (2002).","journal-title":"Structure"},{"key":"918_CR19","doi-asserted-by":"publisher","first-page":"11124","DOI":"10.1073\/pnas.0601924103","volume":"103","author":"Y Tang","year":"2006","unstructured":"Tang, Y., Kim, C.-Y., Mathews, I. I., Cane, D. E. & Khosla, C. The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Proc. Natl Acad. Sci. USA 103, 11124\u201311129 (2006).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"918_CR20","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/S0163-7827(98)00008-3","volume":"37","author":"CE Barry","year":"1998","unstructured":"Barry, C. E. et al. Mycolic acids: structure, biosynthesis and physiological functions. Prog. Lipid Res. 37, 143\u2013179 (1998).","journal-title":"Prog. Lipid Res."},{"key":"918_CR21","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1139\/O07-109","volume":"85","author":"DM Byers","year":"2007","unstructured":"Byers, D. M. & Gong, H. Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family. Biochem. Cell Biol. 85, 649\u2013662 (2007).","journal-title":"Biochem. Cell Biol."},{"key":"918_CR22","doi-asserted-by":"publisher","first-page":"4476","DOI":"10.1021\/acs.biochem.6b00639","volume":"55","author":"T Robbins","year":"2016","unstructured":"Robbins, T., Kapilivsky, J., Cane, D. E. & Khosla, C. Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry 55, 4476\u20134484 (2016).","journal-title":"Biochemistry"},{"key":"918_CR23","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1038\/s41592-020-0731-1","volume":"17","author":"G Pintilie","year":"2020","unstructured":"Pintilie, G. et al. Measurement of atom resolvability in cryo-EM maps with Q-scores. Nat. Methods 17, 328\u2013334 (2020).","journal-title":"Nat. Methods"},{"key":"918_CR24","doi-asserted-by":"publisher","first-page":"16404","DOI":"10.1074\/jbc.M116.730531","volume":"291","author":"M Klaus","year":"2016","unstructured":"Klaus, M. et al. Protein-protein interactions, not substrate recognition, dominate the turnover of chimeric assembly line polyketide synthases. J. Biol. Chem. 291, 16404\u201316415 (2016).","journal-title":"J. Biol. Chem."},{"key":"918_CR25","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1016\/j.jmb.2007.05.022","volume":"372","author":"E Krissinel","year":"2007","unstructured":"Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774\u2013797 (2007).","journal-title":"J. Mol. Biol."},{"key":"918_CR26","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235\u2013242 (2000).","journal-title":"Nucleic Acids Res."},{"key":"918_CR27","doi-asserted-by":"publisher","first-page":"e31486","DOI":"10.7554\/eLife.31486","volume":"7","author":"RM Vernon","year":"2018","unstructured":"Vernon, R. M. et al. Pi-Pi contacts are an overlooked protein feature relevant to phase separation. eLife 7, e31486 (2018).","journal-title":"eLife"},{"key":"918_CR28","doi-asserted-by":"publisher","first-page":"5844","DOI":"10.1039\/c3cp00160a","volume":"15","author":"D Lee","year":"2013","unstructured":"Lee, D., Lee, J. & Seok, C. What stabilizes close arginine pairing in proteins? Phys. Chem. Chem. Phys. 15, 5844\u20135853 (2013).","journal-title":"Phys. Chem. Chem. Phys."},{"key":"918_CR29","doi-asserted-by":"publisher","first-page":"33675","DOI":"10.1074\/jbc.M111.325639","volume":"287","author":"F Bergeret","year":"2012","unstructured":"Bergeret, F. et al. Biochemical and structural study of the atypical acyltransferase domain from the mycobacterial polyketide synthase Pks13. J. Biol. Chem. 287, 33675\u201333690 (2012).","journal-title":"J. Biol. Chem."},{"key":"918_CR30","doi-asserted-by":"publisher","first-page":"44847","DOI":"10.1074\/jbc.M408648200","volume":"279","author":"R Gande","year":"2004","unstructured":"Gande, R. et al. Acyl-CoA carboxylases (accD2 and accD3), together with a unique polyketide synthase (Cg-pks), are key to mycolic acid biosynthesis in Corynebacterianeae such as Corynebacterium glutamicum and Mycobacterium tuberculosis. J. Biol. Chem. 279, 44847\u201344857 (2004).","journal-title":"J. Biol. Chem."},{"key":"918_CR31","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1039\/C5SC01386K","volume":"7","author":"X Lucas","year":"2016","unstructured":"Lucas, X., Bauz\u00e1, A., Frontera, A. & Qui\u00f1onero, D. A thorough anion-\u03c0 interaction study in biomolecules: on the importance of cooperativity effects. Chem. Sci. 7, 1038\u20131050 (2016).","journal-title":"Chem. Sci."},{"key":"918_CR32","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-022-01337-9","volume":"20","author":"C Bon","year":"2022","unstructured":"Bon, C. et al. Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis. BMC Biol. 20, 147 (2022).","journal-title":"BMC Biol."},{"key":"918_CR33","doi-asserted-by":"publisher","first-page":"27292","DOI":"10.1074\/jbc.270.45.27292","volume":"270","author":"KM George","year":"1995","unstructured":"George, K. M., Yuan, Y., Sherman, D. R. & Barry, C. E. The biosynthesis of cyclopropanated mycolic acids in Mycobacterium tuberculosis. Identification and functional analysis of CMAS-2. J. Biol. Chem. 270, 27292\u201327298 (1995).","journal-title":"J. Biol. Chem."},{"key":"918_CR34","doi-asserted-by":"publisher","first-page":"12828","DOI":"10.1073\/pnas.93.23.12828","volume":"93","author":"Y Yuan","year":"1996","unstructured":"Yuan, Y. & Barry, C. E. A common mechanism for the biosynthesis of methoxy and cyclopropyl mycolic acids in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 93, 12828\u201312833 (1996).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"918_CR35","doi-asserted-by":"publisher","first-page":"5981","DOI":"10.1007\/s00216-020-02700-x","volume":"412","author":"L Piersimoni","year":"2020","unstructured":"Piersimoni, L. & Sinz, A. Cross-linking\/mass spectrometry at the crossroads. Anal. Bioanal. Chem. 412, 5981\u20135987 (2020).","journal-title":"Anal. Bioanal. Chem."},{"key":"918_CR36","doi-asserted-by":"publisher","first-page":"3533","DOI":"10.1074\/mcp.M114.042630","volume":"13","author":"RM Kaake","year":"2014","unstructured":"Kaake, R. M. et al. A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells. Mol. Cell Proteom. 13, 3533\u20133543 (2014).","journal-title":"Mol. Cell Proteom"},{"key":"918_CR37","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":"918_CR38","doi-asserted-by":"publisher","first-page":"100132","DOI":"10.1016\/j.mcpro.2021.100132","volume":"20","author":"RM Kaake","year":"2021","unstructured":"Kaake, R. M. et al. Characterization of an A3G-VifHIV-1-CRL5-CBF\u03b2 structure using a cross-linking mass spectrometry pipeline for integrative modeling of host-pathogen complexes. Mol. Cell Proteom. 20, 100132 (2021).","journal-title":"Mol. Cell Proteom."},{"key":"918_CR39","doi-asserted-by":"publisher","first-page":"100743","DOI":"10.1016\/j.jbc.2021.100743","volume":"296","author":"A Sali","year":"2021","unstructured":"Sali, A. From integrative structural biology to cell biology. J. Biol. Chem. 296, 100743 (2021).","journal-title":"J. Biol. Chem."},{"key":"918_CR40","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1002\/pro.3995","volume":"30","author":"DJ Saltzberg","year":"2021","unstructured":"Saltzberg, D. J. et al. Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure. Protein Sci. 30, 250\u2013261 (2021).","journal-title":"Protein Sci."},{"key":"918_CR41","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1007\/978-1-4939-9608-7_15","volume":"2022","author":"D Saltzberg","year":"2019","unstructured":"Saltzberg, D. et al. Modeling biological complexes using integrative modeling platform. Methods Mol. Biol. 2022, 353\u2013377 (2019).","journal-title":"Methods Mol. Biol."},{"key":"918_CR42","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/nature26003","volume":"555","author":"SJ Kim","year":"2018","unstructured":"Kim, S. J. et al. Integrative structure and functional anatomy of a nuclear pore complex. Nature 555, 475\u2013482 (2018).","journal-title":"Nature"},{"key":"918_CR43","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":"918_CR44","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":"918_CR45","doi-asserted-by":"publisher","first-page":"e1001244","DOI":"10.1371\/journal.pbio.1001244","volume":"10","author":"D Russel","year":"2012","unstructured":"Russel, D. et al. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10, e1001244 (2012).","journal-title":"PLoS Biol."},{"key":"918_CR46","doi-asserted-by":"crossref","unstructured":"Tsai, S. C. et al. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc. Natl Acad. Sci. USA 98, 14808\u201314813 (2001).","DOI":"10.1073\/pnas.011399198"},{"key":"918_CR47","doi-asserted-by":"crossref","unstructured":"Gokulan, K., Aggarwal, A., Shipman, L., Besra, G. S. & Sacchettini, J. C. Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations. Acta Crystallogr. D 67, 657\u2013669 (2011).","DOI":"10.1107\/S0907444911020221"},{"key":"918_CR48","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/S0969-2126(03)00004-2","volume":"11","author":"AT Keatinge-Clay","year":"2003","unstructured":"Keatinge-Clay, A. T. et al. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11, 147\u2013154 (2003).","journal-title":"Structure"},{"key":"918_CR49","doi-asserted-by":"publisher","first-page":"12598","DOI":"10.1021\/bi0260177","volume":"41","author":"S-C Tsai","year":"2002","unstructured":"Tsai, S.-C., Lu, H., Cane, D. E., Khosla, C. & Stroud, R. M. Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases. Biochemistry 41, 12598\u201312606 (2002).","journal-title":"Biochemistry"},{"key":"918_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15455-x","volume":"11","author":"JT Mindrebo","year":"2020","unstructured":"Mindrebo, J. T. et al. Gating mechanism of elongating \u03b2-ketoacyl-ACP synthases. Nat. Commun. 11, 1727 (2020).","journal-title":"Nat. Commun."},{"key":"918_CR51","doi-asserted-by":"publisher","first-page":"8862","DOI":"10.1074\/jbc.M408578200","volume":"280","author":"D Portevin","year":"2005","unstructured":"Portevin, D. et al. The acyl-AMP ligase FadD32 and AccD4-containing acyl-CoA carboxylase are required for the synthesis of mycolic acids and essential for mycobacterial growth: identification of the carboxylation product and determination of the acyl-CoA carboxylase components. J. Biol. Chem. 280, 8862\u20138874 (2005).","journal-title":"J. Biol. Chem."},{"key":"918_CR52","doi-asserted-by":"crossref","unstructured":"La Rosa, V. et al. MmpL3 is the cellular target of the antitubercular pyrrole derivative BM212. Antimicrob. Agents Chemother. 56, 324\u2013331 (2012).","DOI":"10.1128\/AAC.05270-11"},{"key":"918_CR53","doi-asserted-by":"publisher","first-page":"e56980","DOI":"10.1371\/journal.pone.0056980","volume":"8","author":"G Poce","year":"2013","unstructured":"Poce, G. et al. Improved BM212 MmpL3 inhibitor analogue shows efficacy in acute murine model of tuberculosis infection. PLoS ONE 8, e56980 (2013).","journal-title":"PLoS ONE"},{"key":"918_CR54","doi-asserted-by":"publisher","unstructured":"LaCava, J., Jiang, H. & Rout, M. P. Protein complex affinity capture from cryomilled mammalian cells. J. Vis. Exp. https:\/\/doi.org\/10.3791\/54518 (2016).","DOI":"10.3791\/54518"},{"key":"918_CR55","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":"918_CR56","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":"918_CR57","doi-asserted-by":"publisher","first-page":"e35383","DOI":"10.7554\/eLife.35383","volume":"7","author":"T Grant","year":"2018","unstructured":"Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife 7, e35383 (2018).","journal-title":"eLife"},{"key":"918_CR58","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1038\/s41592-020-0914-9","volume":"17","author":"TC Terwilliger","year":"2020","unstructured":"Terwilliger, T. C., Ludtke, S. J., Read, R. J., Adams, P. D. & Afonine, P. V. Improvement of cryo-EM maps by density modification. Nat. Methods 17, 923\u2013927 (2020).","journal-title":"Nat. Methods"},{"key":"918_CR59","doi-asserted-by":"crossref","unstructured":"Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531\u2013544 (2018).","DOI":"10.1107\/S2059798318006551"},{"key":"918_CR60","doi-asserted-by":"publisher","first-page":"e42166","DOI":"10.7554\/eLife.42166","volume":"7","author":"J Zivanov","year":"2018","unstructured":"Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).","journal-title":"eLife"},{"key":"918_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\u2014a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"918_CR62","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1002\/pro.3235","volume":"27","author":"TD Goddard","year":"2018","unstructured":"Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14\u201325 (2018).","journal-title":"Protein Sci."},{"key":"918_CR63","doi-asserted-by":"crossref","unstructured":"Terwilliger, T. C., Sobolev, O. V., Afonine, P. V. & Adams, P. D. Automated map sharpening by maximization of detail and connectivity. Acta Crystallogr. D 74, 545\u2013559 (2018).","DOI":"10.1107\/S2059798318004655"},{"key":"918_CR64","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":"918_CR65","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/nprot.2015.053","volume":"10","author":"LA Kelley","year":"2015","unstructured":"Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845\u2013858 (2015).","journal-title":"Nat. Protoc."},{"key":"918_CR66","doi-asserted-by":"crossref","unstructured":"Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486\u2013501 (2010).","DOI":"10.1107\/S0907444910007493"},{"key":"918_CR67","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 74, 519\u2013530 (2018).","DOI":"10.1107\/S2059798318002425"},{"key":"918_CR68","doi-asserted-by":"crossref","unstructured":"van Zundert, G. C. P., Moriarty, N. W., Sobolev, O. V., Adams, P. D., & Borrelli, K. W. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix\/OPLS3e for improved structure and ligand quality. Structure 29, 913\u2013921.e4 (2021).","DOI":"10.1016\/j.str.2021.03.011"},{"key":"918_CR69","doi-asserted-by":"publisher","first-page":"W368","DOI":"10.1093\/nar\/gky309","volume":"46","author":"L Pravda","year":"2018","unstructured":"Pravda, L. et al. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46, W368\u2013W373 (2018).","journal-title":"Nucleic Acids Res."},{"key":"918_CR70","doi-asserted-by":"publisher","first-page":"16504","DOI":"10.1073\/pnas.1212797109","volume":"109","author":"BK Tan","year":"2012","unstructured":"Tan, B. K. et al. Discovery of a cardiolipin synthase utilizing phosphatidylethanolamine and phosphatidylglycerol as substrates. Proc. Natl Acad. Sci. USA 109, 16504\u201316509 (2012).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"918_CR71","doi-asserted-by":"publisher","first-page":"M110.002212","DOI":"10.1074\/mcp.M110.002212","volume":"10","author":"A Kao","year":"2011","unstructured":"Kao, A. et al. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol. Cell Proteom. 10, M110.002212 (2011).","journal-title":"Mol. Cell Proteom."},{"key":"918_CR72","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1038\/nbt.2377","volume":"30","author":"MC Chambers","year":"2012","unstructured":"Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918\u2013920 (2012).","journal-title":"Nat. Biotechnol."},{"key":"918_CR73","doi-asserted-by":"publisher","first-page":"2534","DOI":"10.1093\/bioinformatics\/btn323","volume":"24","author":"D Kessner","year":"2008","unstructured":"Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534\u20132536 (2008).","journal-title":"Bioinformatics"},{"key":"918_CR74","doi-asserted-by":"publisher","first-page":"D442","DOI":"10.1093\/nar\/gky1106","volume":"47","author":"Y Perez-Riverol","year":"2019","unstructured":"Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442\u2013D450 (2019).","journal-title":"Nucleic Acids Res."},{"key":"918_CR75","doi-asserted-by":"publisher","first-page":"1392","DOI":"10.1074\/mcp.O113.037200","volume":"13","author":"PR Baker","year":"2014","unstructured":"Baker, P. R. & Chalkley, R. J. MS-viewer: a web-based spectral viewer for proteomics results. Mol. Cell Proteom. 13, 1392\u20131396 (2014).","journal-title":"Mol. Cell Proteom."},{"key":"918_CR76","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1038\/nature06404","volume":"450","author":"F Alber","year":"2007","unstructured":"Alber, F. et al. Determining the architectures of macromolecular assemblies. Nature 450, 683\u2013694 (2007).","journal-title":"Nature"},{"key":"918_CR77","doi-asserted-by":"publisher","first-page":"2344","DOI":"10.1016\/j.bpj.2017.10.005","volume":"113","author":"S Viswanath","year":"2017","unstructured":"Viswanath, S., Chemmama, I. E., Cimermancic, P. & Sali, A. Assessing exhaustiveness of stochastic sampling for integrative modeling of macromolecular structures. Biophys. J. 113, 2344\u20132353 (2017).","journal-title":"Biophys. J."}],"container-title":["Nature Structural &amp; Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41594-022-00918-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-022-00918-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-022-00918-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,17]],"date-time":"2023-03-17T13:09:23Z","timestamp":1679058563000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41594-022-00918-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,13]]},"references-count":77,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,3]]}},"alternative-id":["918"],"URL":"https:\/\/doi.org\/10.1038\/s41594-022-00918-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.01.27.525930","asserted-by":"object"}]},"ISSN":["1545-9993","1545-9985"],"issn-type":[{"value":"1545-9993","type":"print"},{"value":"1545-9985","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,13]]},"assertion":[{"value":"8 February 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 December 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 February 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The Krogan Laboratory has received research support from Vir Biotechnology, F. Hoffmann-La Roche and Rezo Therapeutics. N.J.K. has financially compensated consulting agreements with the Icahn School of Medicine at Mount Sinai, New York, Maze Therapeutics, Interline Therapeutics, Rezo Therapeutics, GEn1E Lifesciences, Inc. and Twist Bioscience Corp. He is on the Board of Directors of Rezo Therapeutics and is a shareholder in Tenaya Therapeutics, Maze Therapeutics, Rezo Therapeutics and Interline Therapeutics.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}