Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2022-03-16 2022-09-21 2022-09-21 2026-09-02 Not funded 25541 Austria Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state Kravchuk V Kampjut D Sazanov L Complex I, NADH, Quinone, PROTON TRANSPORT Kravchuk V Petrova O Kampjut D Wojciechowska-Bason A Breese Z Sazanov L A universal coupling mechanism of respiratory complex I. Nature UK 609 808 814 2022 36104567 doi:10.1038/s41586-022-05199-7 1476-4687 0006 NATUAS EMD-14815 other EM volume

Consensus map

EMD-14816 other EM volume

Focused refinement

EMD-14817 other EM volume

Focused refinement

7z7v FULLOVERLAP EMDB EMD-14538 associated EM volume

Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state

EMDB EMD-14815 other EM volume

Consensus map

EMDB EMD-14816 other EM volume

Focused refinement

EMDB EMD-14817 other EM volume

Focused refinement

Complex I Complex I 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Escherichia coli str. K-12 substr. MC4100 NADH-quinone oxidoreductase subunit F Escherichia coli str. K-12 substr. MC4100 0.049352332 1 LEVO MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDE SMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNI MGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSR LGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAH APGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW A0A037YNA7 7.1.1.- NADH dehydrogenase I subunit E Escherichia coli str. K-12 substr. MC4100 0.018614048999999997 1 LEVO MHENQQPQTEAFELSAAEREAIEHEMHHYEDPRAASIEALKIVQKQRGWVPDGAIHAIADVLGIPASDVEGVATFYSQIF RQPVGRHVIRYCDSVVCHINGYQGIQAALEKKLNIKPGQTTFDGRFTLLPTCCLGNCDKGPNMMIDEDTHAHLTPEAIPE LLERYK A0A829CRH1 NADH-quinone oxidoreductase Escherichia coli str. K-12 substr. MC4100 0.100419211 1 LEVO MATIHVDGKEYEVNGADNLLEACLSLGLDIPYFCWHPALGSVGACRQCAVKQYQNAEDTRGRLVMSCMTPASDGTFISID DEEAKQFRESVVEWLMTNHPHDCPVCEEGGNCHLQDMTVMTGHSFRRYRFTKRTHRNQDLGPFISHEMNRCIACYRCVRY YKDYADGTDLGVYGAHDNVYFGRPEDGTLESEFSGNLVEICPTGVFTDKTHSERYNRKWDMQFAPSICQQCSIGCNISPG ERYGELRRIENRYNGTVNHYFLCDRGRFGYGYVNLKDRPRQPVQRRGDDFITLNAEQAMQGAADILRQSKKVIGIGSPRA SVESNFALRELVGEENFYTGIAHGEQERLQLALKVLREGGIYTPALREIESYDAVLVLGEDVTQTGARVALAVRQAVKGK AREMAAAQKVADWQIAAILNIGQRAKHPLFVTNVDDTRLDDIAAWTYRAPVEDQARLGFAIAHALDNSAPAVDGIEPELQ SKIDVIVQALAGAKKPLIISGTNAGSLEVIQAAANVAKALKGRGADVGITMIARSVNSMGLGIMGGGSLEEALTELETGR ADAVVVLENDLHRHASAIRVNAALAKAPLVMVVDHQRTAIMENAHLVLSAASFAESDGTVINNEGRAQRFFQVYDPAYYD SKTVMLESWRWLHSLHSTLLSREVDWTQLDHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANIS VHEPRQPQDIDTMFTFSMEGNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVP ARFQPQDGKWRIAPYYHLFGSDELSQRAPVFQSRMPQPYIKLNPADAAKLGVNAGTRVSFSYDGNTVTLPVEIAEGLTAG QVGLPMGMSGIAPVLAGAHLEDLKEAQQ A0A037YPU0 7.1.1.- NADH-quinone oxidoreductase subunit C/D Escherichia coli str. K-12 substr. MC4100 0.06832194500000001 1 LEVO MTDLTAQEPAWQTRDHLDDPVIGELRNRFGPDAFTVQATRTGVPVVWIKREQLLEVGDFLKKLPKPYVMLFDLHGMDERL RTHREGLPAADFSVFYHLISIDRNRDIMLKVALAENDLHVPTFTKLFPNANWYERETWDLFGITFDGHPNLRRIMMPQTW KGHPLRKDYPARATEFSPFELTKAKQDLEMEALTFKPEEWGMKRGTENEDFMFLNLGPNHPSAHGAFRIVLQLDGEEIVD CVPDIGYHHRGAEKMGERQSWHSYIPYTDRIEYLGGCVNEMPYVLAVEKLAGITVPDRVNVIRVMLSELFRINSHLLYIS TFIQDVGAMTPVFFAFTDRQKIYDLVEAITGFRMHPAWFRIGGVAHDLPRGWDRLLREFLDWMPKRLASYEKAALQNTIL KGRSQGVAAYGAKEALEWGTTGAGLRATGIDFDVRKARPYSGYENFDFEIPVGGGVSDCYTRVMLKVEELRQSLRILEQC LNNMPEGPFKADHPLTTPPPKERTLQHIETLITHFLQVSWGPVMPANESFQMIEATKGINSYYLTSDGSTMSYRTRVRTP SFAHLQQIPAAIRGSLVSDLIVYLGSIDFVMSDVDR A0A024L1E0 7.1.1.- NADH-quinone oxidoreductase subunit B Escherichia coli str. K-12 substr. MC4100 0.025081809 1 LEVO MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVAR FGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPP RPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI V0ZV11 7.1.1.- NADH-quinone oxidoreductase subunit I Escherichia coli str. K-12 substr. MC4100 0.020562771 1 LEVO MTLKELLVGFGTQVRSIWMIGLHAFAKRETRMYPEEPVYLPPRYRGRIVLTRDPDGEERCVACNLCAVACPVGCISLQKA ETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDFEMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDG KDKGEAENEAKPIDVKSLLP A0A1X3LLK1 NADH-quinone oxidoreductase subunit H Escherichia coli str. K-12 substr. MC4100 0.036240921999999995 1 LEVO MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDR VIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFL GLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVG EYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVI LWQAQ E6BKM7 7.1.1.- NADH-quinone oxidoreductase subunit A Escherichia coli str. K-12 substr. MC4100 0.016474283 1 LEVO MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDV EALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARSRRERMNPETNSIANRQR A0A862ZI24 7.1.1.- NADH dehydrogenase subunit L Escherichia coli str. K-12 substr. MC4100 0.066483609 1 LEVO MNMLALTIILPLIGFVLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQTYSQPLWTWMSVGDFNIGFNLV LDGLSLTMLSVVTGVGFLIHMYASWYMRGEEGYSRFFAYTNLFIASMVVLVLADNLLLMYLGWEGVGLCSYLLIGFYYTD PKNGAAAMKAFVVTRVGDVFLAFALFILYNELGTLNFREMVELAPAHFADGNNMLMWATLMLLGGAVGKSAQLPLQTWLA DAMAGPTPVSALIHAATMVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMF LALGVQAWDAAIFHLMTHAFFKALLFLASGSVILACHHEQNIFKMGGLRKSIPLVYLCFLVGGAALSALPLVTAGFFSKD EILAGAMANGHINLMVAGLVGAFMTSLYTFRMIFIVFHGKEQIHAHAVKGVTHSLPLIVLLILSTFVGALIVPPLQGVLP QTTELAHGSMLTLEITSGVVAVVGILLAAWLWLGKRTLVTSIANSAPGRLLGTWWYNAWGFDWLYDKVFVKPFLGIAWLL KRDPLNSMMNIPAVLSRFAGKGLLLSENGYLRWYVASMSIGAVVVLALLMVLR A0A024L0E1 1.6.5.11 NADH dehydrogenase I subunit M Escherichia coli str. K-12 substr. MC4100 0.05656008999999999 1 LEVO MLLPWLILIPFIGGFLCWQTERFGVKVPRWIALITMGLTLALSLQLWLQGGYSLTQSAGIPQWQSEFDMPWIPRFGISIH LAIDGLSLLMVVLTGLLGVLAVLCSWKEIEKYQGFFHLNLMWILGGVIGVFLAIDMFLFFFFWEMMLVPMYFLIALWGHK ASDGKTRITAATKFFIYTQASGLVMLIAILALVFVHYNATGVWTFNYEELLNTPMSSGVEYLLMLGFFIAFAVKMPVVPL HGWLPDAHSQAPTAGSVDLAGILLKTAAYGLLRFSLPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSV SHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERIHTRDMRMMGGLWSKMKWLPALSLFFAVATLGMPG TGNFVGEFMILFGSFQVVPVITVISTFGLVFASVYSLAMLHRAYFGKAKSQIASQELPGMSLRELFMILLLVVLLVLLGF YPQPILDTSHSAIGNIQQWFVNSVTTTRP C3T2G7 NADH-quinone oxidoreductase subunit N Escherichia coliEscherichia coli str. K-12 substr. MC4100 0.05207267199999999 1 LEVO MTITPQNLIALLPLLIVGLTVVVVMLSIAWRRNHFLNATLSVIGLNAALVSLWFVGQAGAMDVTPLMRVDGFAMLYTGLV LLASLATCTFAYPWLEGYNDNKDEFYLLVLIAALGGILLANANHLASLFLGIELISLPLFGLVGYAFRQKRSLEASIKYT ILSAAASSFLLFGMALVYAQSGDLSFVALGKNLGDGMLNEPLLLAGFGLMIVGLGFKLSLVPFHLWTPDVYQGAPAPVST FLATASKIAIFGVVMRLFLYAPVGDSEAIRVVLAIIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIALQTGE MSMEAVGVYLAGYLFSSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMTVMMLSLAGIPMTLGFIGKFYVLA VGVQAHLWWLVGAVVVGSAIGLYYYLRVAVSLYLHAPEQPGRDAPSNWQYSAGGIVVLISALLVLVLGVWPQPLISIVRL AMPLM E2QPD7 7.1.1.- NADH-quinone oxidoreductase subunit K Escherichia coli str. K-12 substr. MC4100 0.010852961 1 LEVO MIPLQHGLILAAILFVLGLTGLVIRRNLLFMLIGLEIMINASALAFVVAGSYWGQTDGQVMYILAISLAAAEASIGLALL LQLHRRRQNLNIDSVSEMRG A0A7U9LRT0 7.1.1.- NADH-quinone oxidoreductase subunit J Escherichia coli str. K-12 substr. MC4100 0.019889551 1 LEVO MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYAGAIMVLFVFVVMMLNLGGSE IEQERQWLKPQVWIGPAILSAIMLVVIVYAILGVNDQGIDGTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGR EERAGEVLSNRKDDSAKRKTEEHA A0A0H3MIP2 7.1.1.- IRON/SULFUR CLUSTER 0.00035163999999999996 7 SF4 FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE 0.000665441 1 NAI FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES CALCIUM ION 4.0078e-05 1 CA 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 12 3PE EICOSANE 0.000282547 3 LFA TETRADECANE 0.000198388 1 C14 water 1.8015e-05 1297 HOH singleParticle particle 0.25 6.0 20.0 C6H13NO4S MES 2.0 CaCl2 calcium chloride 250.0 NaCl sodium chloride 0.01 C47H88O22 LMNG 0.25 C40H80NO8P E. coli lipid extract 0.1 C32H58N2O7S CHAPS 2.0 C21H27N7O14P2 NADH 0.8 C19H30O4 DQ Quantifoil R0.6/1 CARBON CONTINUOUS 0.9 GLOW DISCHARGE 10 ETHANE 100 288 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 2.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 11316 80.0 1 4483166 CTFFIND PHASE FLIPPING AND AMPLITUDE CORRECTION 4HEA 2.29 FSC 0.143 CUT-OFF RELION 317174 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION emd_14538.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 306 421 475 0 0 0 306 421 475 153.0 210.5 237.5 90.0 90.0 90.0 X Y Z -0.104417 0.7481791 0.0052255583 0.025032891 0.5 0.5 0.5 0.06 AUTHOR ::::EMDATABANK.org::::EMD-14538:::: 4HEA PDB experimental model 3RKO PDB experimental model FLEXIBLE FIT ML REAL emd_14538_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 504 504 504 0 0 0 504 504 504 534.24 534.24 534.24 90.0 90.0 90.0 X Y Z -0.24160396 0.69702405 0.0000012724798 0.005358897 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-14538:::: Open-ready PA focused emd_14538_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 504 504 504 0 0 0 504 504 504 534.24 534.24 534.24 90.0 90.0 90.0 X Y Z -0.1953307 0.37006465 0.0000035003086 0.004640835 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-14538:::: Open-ready MD focused