Respiratory complex I from Escherichia coli

2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _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 REFINEMENT_DESCRIPTION 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_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2021-03-23 2021-08-25 2021-08-25 2026-09-16 European Research Council (ERC) 00281ROEF Belgium Respiratory complex I from Escherichia coli - conformation 1 Kolata P Efremov RG NADH:ubiquinone reductase (H+-translocating), oxidative phosphorylation, ELECTRON TRANSPORT Kolata P Efremov RG Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation. Elife US 10 2021 34308841 doi:10.7554/eLife.68710 2050-084X EMD-13291 other EM volume

Respiratory Complex I from Escherichia coli solubilised in LMNG

EMD-12661 other EM volume

Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm

EMD-12652 other EM volume

Respiratory complex I from Escherichia coli - focused refinement of membrane arm

EMD-12654 other EM volume

Respiratory complex I from Escherichia coli - conformation 2

EMD-12655 other EM volume

Respiratory complex I from Escherichia coli - conformation 3

7nyr FULLOVERLAP EMDB EMD-12653 associated EM volume

Respiratory complex I from Escherichia coli - conformation 1

EMDB EMD-13291 other EM volume

Respiratory Complex I from Escherichia coli solubilised in LMNG

EMDB EMD-12661 other EM volume

Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm

EMDB EMD-12652 other EM volume

Respiratory complex I from Escherichia coli - focused refinement of membrane arm

EMDB EMD-12654 other EM volume

Respiratory complex I from Escherichia coli - conformation 2

EMDB EMD-12655 other EM volume

Respiratory complex I from Escherichia coli - conformation 3

PDB 7NZ1 unspecified

Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm

PDB 7NYH unspecified

Respiratory complex I from Escherichia coli - focused refinement of membrane arm

PDB 7NYU unspecified

Respiratory complex I from Escherichia coli - conformation 2

PDB 7NYV unspecified

Respiratory complex I from Escherichia coli - conformation 3

Respiratory complex I from Escherichia coli - conformation 1 Respiratory complex I from Escherichia coli - conformation 1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Escherichia coli B BL21(AI) cell membrane 0.55 NADH-quinone oxidoreductase subunit B Escherichia coli B BL21(AI) 0.025097809 1 LEVO MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVAR FGAEVLRASPRQADLMVVAGT(CSX)FTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIP GCPPRPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI P0AFC7 7.1.1.- NADH-quinone oxidoreductase subunit C/D Escherichia coli B BL21(AI) 0.06832194500000001 1 LEVO MTDLTAQEPAWQTRDHLDDPVIGELRNRFGPDAFTVQATRTGVPVVWIKREQLLEVGDFLKKLPKPYVMLFDLHGMDERL RTHREGLPAADFSVFYHLISIDRNRDIMLKVALAENDLHVPTFTKLFPNANWYERETWDLFGITFDGHPNLRRIMMPQTW KGHPLRKDYPARATEFSPFELTKAKQDLEMEALTFKPEEWGMKRGTENEDFMFLNLGPNHPSAHGAFRIVLQLDGEEIVD CVPDIGYHHRGAEKMGERQSWHSYIPYTDRIEYLGGCVNEMPYVLAVEKLAGITVPDRVNVIRVMLSELFRINSHLLYIS TFIQDVGAMTPVFFAFTDRQKIYDLVEAITGFRMHPAWFRIGGVAHDLPRGWDRLLREFLDWMPKRLASYEKAALQNTIL KGRSQGVAAYGAKEALEWGTTGAGLRATGIDFDVRKARPYSGYENFDFEIPVGGGVSDCYTRVMLKVEELRQSLRILEQC LNNMPEGPFKADHPLTTPPPKERTLQHIETLITHFLQVSWGPVMPANESFQMIEATKGINSYYLTSDGSTMSYRTRVRTP SFAHLQQIPAAIRGSLVSDLIVYLGSIDFVMSDVDR P33599 7.1.1.2 NADH-quinone oxidoreductase subunit E Escherichia coli B BL21(AI) 0.018630049 1 LEVO MHENQQPQTEAFELSAAEREAIEHEMHHYEDPRAASIEALKIVQKQRGWVPDGAIHAIADVLGIPASDVEGVATFYSQIF RQPVGRHVIRYCDSVVCHINGYQGIQAALEKKLNIKPGQTTFDGRFTLLPT(CSX)CLGNCDKGPNMMIDEDTHAHLTPE AIPELLERYK P0AFD1 7.1.1.2 NADH-quinone oxidoreductase subunit F Escherichia coli B BL21(AI) 0.049368332 1 LEVO MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDE SMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNI MGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAWGKPT(CSX)VNNVETLCNVPAILANGVEWY QNISKSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGK AGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKT FCAHAPGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW P31979 7.1.1.2 NADH-quinone oxidoreductase subunit G Escherichia coli B BL21(AI) 0.100419211 1 LEVO MATIHVDGKEYEVNGADNLLEACLSLGLDIPYFCWHPALGSVGACRQCAVKQYQNAEDTRGRLVMSCMTPASDGTFISID DEEAKQFRESVVEWLMTNHPHDCPVCEEGGNCHLQDMTVMTGHSFRRYRFTKRTHRNQDLGPFISHEMNRCIACYRCVRY YKDYADGTDLGVYGAHDNVYFGRPEDGTLESEFSGNLVEICPTGVFTDKTHSERYNRKWDMQFAPSICQQCSIGCNISPG ERYGELRRIENRYNGTVNHYFLCDRGRFGYGYVNLKDRPRQPVQRRGDDFITLNAEQAMQGAADILRQSKKVIGIGSPRA SVESNFALRELVGEENFYTGIAHGEQERLQLALKVLREGGIYTPALREIESYDAVLVLGEDVTQTGARVALAVRQAVKGK AREMAAAQKVADWQIAAILNIGQRAKHPLFVTNVDDTRLDDIAAWTYRAPVEDQARLGFAIAHALDNSAPAVDGIEPELQ SKIDVIVQALAGAKKPLIISGTNAGSLEVIQAAANVAKALKGRGADVGITMIARSVNSMGLGIMGGGSLEEALTELETGR ADAVVVLENDLHRHASAIRVNAALAKAPLVMVVDHQRTAIMENAHLVLSAASFAESDGTVINNEGRAQRFFQVYDPAYYD SKTVMLESWRWLHSLHSTLLSREVDWTQLDHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANIS VHEPRQPQDIDTMFTFSMEGNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVP ARFQPQDGKWRIAPYYHLFGSDELSQRAPVFQSRMPQPYIKLNPADAAKLGVNAGTRVSFSYDGNTVTLPVEIAEGLTAG QVGLPMGMSGIAPVLAGAHLEDLKEAQQ P33602 7.1.1.2 NADH-quinone oxidoreductase subunit I Escherichia coli B BL21(AI) 0.020562771 1 LEVO MTLKELLVGFGTQVRSIWMIGLHAFAKRETRMYPEEPVYLPPRYRGRIVLTRDPDGEERCVACNLCAVACPVGCISLQKA ETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDFEMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDG KDKGEAENEAKPIDVKSLLP P0AFD6 7.1.1.2 NADH-quinone oxidoreductase subunit K Escherichia coli B BL21(AI) 0.010852961 1 LEVO MIPLQHGLILAAILFVLGLTGLVIRRNLLFMLIGLEIMINASALAFVVAGSYWGQTDGQVMYILAISLAAAEASIGLALL LQLHRRRQNLNIDSVSEMRG P0AFE4 7.1.1.- NADH-quinone oxidoreductase subunit J Escherichia coli B BL21(AI) 0.019889551 1 LEVO MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYAGAIMVLFVFVVMMLNLGGSE IEQERQWLKPQVWIGPAILSAIMLVVIVYAILGVNDQGIDGTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGR EERAGEVLSNRKDDSAKRKTEEHA P0AFE0 7.1.1.- NADH-quinone oxidoreductase subunit A Escherichia coli B BL21(AI) 0.016474283 1 LEVO MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDV EALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARSRRERMNPETNSIANRQR P0AFC3 7.1.1.- NADH-quinone oxidoreductase subunit H Escherichia coli B BL21(AI) 0.036240921999999995 1 LEVO MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDR VIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFL GLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVG EYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVI LWQAQ P0AFD4 7.1.1.- NADH-quinone oxidoreductase subunit M Escherichia coli B BL21(AI) 0.05656008999999999 1 LEVO MLLPWLILIPFIGGFLCWQTERFGVKVPRWIALITMGLTLALSLQLWLQGGYSLTQSAGIPQWQSEFDMPWIPRFGISIH LAIDGLSLLMVVLTGLLGVLAVLCSWKEIEKYQGFFHLNLMWILGGVIGVFLAIDMFLFFFFWEMMLVPMYFLIALWGHK ASDGKTRITAATKFFIYTQASGLVMLIAILALVFVHYNATGVWTFNYEELLNTPMSSGVEYLLMLGFFIAFAVKMPVVPL HGWLPDAHSQAPTAGSVDLAGILLKTAAYGLLRFSLPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSV SHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERIHTRDMRMMGGLWSKMKWLPALSLFFAVATLGMPG TGNFVGEFMILFGSFQVVPVITVISTFGLVFASVYSLAMLHRAYFGKAKSQIASQELPGMSLRELFMILLLVVLLVLLGF YPQPILDTSHSAIGNIQQWFVNSVTTTRP P0AFE8 7.1.1.- NADH-quinone oxidoreductase subunit L Escherichia coli B BL21(AI) 0.066513633 1 LEVO MNMLALTIILPLIGFVLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQTYSQPLWTWMSVGDFNIGFNLV LDGLSLTMLSVVTGVGFLIHMYASWYMRGEEGYSRFFAYTNLFIASMVVLVLADNLLLMYLGWEGVGLCSYLLIGFYYTD PKNGAAAMKAFVVTRVGDVFLAFALFILYNELGTLNFREMVELAPAHFADGNNMLMWATLMLLGGAVGKSAQLPLQTWLA DAMAGPTPVSALIHAATMVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMF LALGVQAWDAAIFHLMTHAFFKALLFLASGSVILACHHEQNIFKMGGLRKSIPLVYLCFLVGGAALSALPLVTAGFFSKD EILAGAMANGHINLMVAGLVGAFMTSLYTFRMIFIVFHGKEQIHAHAVKGVTHSLPLIVLLILSTFVGALIVPPLQGVLP QTTELAHGSMLTLEITSGVVAVVGILLAAWLWLGKRTLVTSIANSAPGRLLSTWWYNAWGFDWLYDKVFVKPFLGIAWLL KRDPLNSMMNIPAVLSRFAGKGLLLSENGYLRWYVASMSIGAVVVLALLMVLR A0A1V3W1N5 1.6.5.11 NADH-quinone oxidoreductase subunit N Escherichia coli B BL21(AI) 0.05207267199999999 1 LEVO MTITPQNLIALLPLLIVGLTVVVVMLSIAWRRNHFLNATLSVIGLNAALVSLWFVGQAGAMDVTPLMRVDGFAMLYTGLV LLASLATCTFAYPWLEGYNDNKDEFYLLVLIAALGGILLANANHLASLFLGIELISLPLFGLVGYAFRQKRSLEASIKYT ILSAAASSFLLFGMALVYAQSGDLSFVALGKNLGDGMLNEPLLLAGFGLMIVGLGFKLSLVPFHLWTPDVYQGAPAPVST FLATASKIAIFGVVMRLFLYAPVGDSEAIRVVLAIIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIALQTGE MSMEAVGVYLAGYLFSSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMTVMMLSLAGIPMTLGFIGKFYVLA VGVQAHLWWLVGAVVVGSAIGLYYYLRVAVSLYLHAPEQPGRDAPSNWQYSAGGIVVLISALLVLVLGVWPQPLISIVRL AMPLM P0AFF0 7.1.1.- IRON/SULFUR CLUSTER 0.00035163999999999996 7 SF4 FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN CALCIUM ION 4.0078e-05 1 CA singleParticle particle 0.1 6.8 20.0 C8H19NO5 Bis-Tris 200.0 NaCl Sodium chloride 2.0 CaCl2 Calcium chloride

The buffer was used for gel filtration of protein reconstituted in lipid nanodiscs

Quantifoil R0.6/1 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE 240 AIR 0.028 ETHANE 97 296 GATAN CRYOPLUNGE 3 JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.55 0.9 2.2 60000.0 JEOL CRYOSPECPORTER NITROGEN In-column Omega Filter 20 GATAN K3 (6k x 4k) 9122 3.0 64.7 1 1256734 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.3 FSC 0.143 CUT-OFF RELION 3.1 PHENIX 1.18.2 23445 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_12653.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 370.17603 370.17603 370.17603 90.0 90.0 90.0 Z Y X -51.738869999999999 177.749860000000012 0.00078837137 1.0001967 1.1568 1.1568 1.1568 1.19 AUTHOR ::::EMDATABANK.org::::EMD-12653:::: 4HEA PDB experimental model 3RKO PDB experimental model FLEXIBLE FIT Correlation coefficient REAL 50.0 emd_12653_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 370.17603 370.17603 370.17603 90.0 90.0 90.0 X Y Z -0.08339649 0.21284986 0.000045671426 0.008387188 1.1568 1.1568 1.1568 AUTHOR ::::EMDATABANK.org::::EMD-12653:::: emd_12653_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 370.17603 370.17603 370.17603 90.0 90.0 90.0 X Y Z -0.08503716 0.20541252 -0.000028039705 0.008261031 1.1568 1.1568 1.1568 AUTHOR ::::EMDATABANK.org::::EMD-12653::::