2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _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 PDBe PDBe 2023-08-25 2024-09-11 2024-09-11 2026-09-16 Medical Research Council (MRC, United Kingdom) MC_UU_00015/2 United Kingdom Medical Research Council (MRC, United Kingdom) MC_UU_00028/1 United Kingdom Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs Ivanov BS Bridges HR Hirst J Respiratory complex I, NADH:ubiquinone oxidoreductase, Nanodiscs, OXIDOREDUCTASE Ivanov BS Bridges HR Jarman OD Hirst J Structure of the turnover-ready state of an ancestral respiratory complex I. Nat Commun UK 15 9340 9340 2024 39472559 doi:10.1038/s41467-024-53679-3 2041-1723 8qby FULLOVERLAP EMDB EMD-18324 associated EM volume
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
 Respiratory complex I Respiratory complex I 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Paracoccus denitrificans PD1222 NADH-quinone oxidoreductase subunit K Paracoccus denitrificans PD1222 0.010863054 1 LEVO MIGLTHYLVVGAILFVTGIFGIFVNRKNVIVILMSIELMLLAVNINFVAFSTHLGDLAGQVFTMFVLTVAAAEAAIGLAI LVVFFRNRGTIAVEDVNVMKG A1B482 7.1.1.- NADH-quinone oxidoreductase Paracoccus denitrificans PD1222 0.07328939799999999 1 LEVO MADLRKIKIDDTIIEVDPNMTLIQACEMAGIEVPRFCYHERLSIAGNCRMCLVEVVGGPPKPAASCAMQVKDLRPGPEGA PSEIRTNSPMVKKAREGVMEFLLINHPLDCPICDQGGECDLQDQAMAYGVDFSRYREPKRATEDLNLGPLVETHMTRCIS CTRCVRFTTEVAGITQMGQTGRGEDSEITSYLNQTLESNMQGNIIDLCPVGALVSKPYAFTARPWELTKTESIDVMDALG SSIRIDTKGREVMRILPRNHDGVNEEWISDKTRFVWDGLRRQRLDRPYIRENGRLRPASWPEALEAAARAMKGKKIAGLI GDLVPAEAAFSLKQLVEGLGGKVECRVDGARLPAGNRSAYVGTARIEDIDDAEMIQLIGTNPRDEAPVLNARIRKAWSKG AKVGLVGEPVDLTYDYAHVGTDRAALESLSSREISDETKARPSIVIVGQGAIREADGEAVLAHAMKLAENSNSGLLILHT AAGRVGAMDVGAVTEGGLLAAIDGAEVVYNLGADEVDIDQGPFVIYQGSHGDRGAHRADIILPGACYTEESGLFVNTEGR PQLAMRANFAPGEGKENWAILRALSAELGATQPWDSLAGLRRKLVEAVPHLAQIDQVPQNEWQPLGRFDLGQASFRYAIR DFYLTNPIARSSPLMGELSAMAAARKAPAPLAAE A1B489 7.1.1.- Protein-L-isoaspartate O-methyltransferase Paracoccus denitrificans PD1222 0.023528946999999998 1 LEVO MTDFAQRRTMMVDTQVRPNEVTSYPVIEAMLNVPREQFVPESRRDVAYVGNNIDLAPGRVLLEPRTLGKMMDILNLQNGD LVLDVGCGYGYSAAVMARIAEAVVAVEEDAAMAAEAEGRLAAQDVFNVAVVQGALAEGCPGQAPYDAILIEGAVEQVPEA LTEQLREGGRIVALFREGNLGIVRLGHKLDGRVNWRFAFNAVAPLLPGFARPRGFVL A1B5L6 NADH-quinone oxidoreductase subunit I Paracoccus denitrificans PD1222 0.018925561 1 LEVO MAFDFARATKYFLMWDFIKGFGLGMRYFVSPKPTLNYPHEKGPLSPRFRGEHALRRYPNGEERCIACKLCEAVCPAQAIT IDAEPREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYATETREELFYDKQKLLANGERWEAEIARNLQLDA PYR A1B486 NADH dehydrogenase subunit E Paracoccus denitrificans PD1222 0.026145865 1 LEVO MLRRLSPIQPDSFEFTPANLEWARAQMTKYPEGRQQSAIIPVLWRAQEQEGWLSRPAIEYCADLLGMPYIRALEVATFYF MFQLQPVGSVAHIQICGTTTCMICGAEDLIRVCKEKIAPEPHALSADGRFSWEEVECLGACTNAPMAQIGKDFYEDLTVE KLAALIDRFAAGEVPVPGPQNGRFSAEALGGPTALADLKGGEAHNASVARALRLGDSIKRIDGTEVPITTPWLATQNGV A1B494 NADH-quinone oxidoreductase subunit N Paracoccus denitrificans PD1222 0.05256482 1 LEVO MTSLDFSTILPEVVLAGYALAALMAGAYLGKDRLARTLLWVTVAAFLVVAAMVGLGNHVDGAAFHGMFIDDGFSRFAKVV TLVAAAGVLAMSADYMQRRNMLRFEFPIIVALAVLGMMFMVSAGDLLTLYMGLELQSLALYVVAAMRRDSVRSSEAGLKY FVLGSLSSGLLLYGASLVYGFAGTTGFEGIISTIEAGHLSLGVLFGLVFMLVGLSFKVSAVPFHMWTPDVYEGSPTPVTA FFATAPKVAAMALIARLVFDAFGHVIGDWSQIVAALAVMSMFLGSIAGIGQTNIKRLMAYSSIAHMGFALVGLAAGTAIG VQNMLLYMTIYAVMNIGTFAFILSMERDGVPVTDLAALNRFAWTDPVKALAMLVLMFSLAGVPPTLGFFAKFGVLTAAVD AGMGWLAVLGVIASVIGAFYYLRIVYYMYFGGESEGMTSRMGAVQYLALMVPALAMLVGAISMFGVDSAAGRAAETLVGP VAAIEQPAEAAQAEPVQGE A1B479 NADH-quinone oxidoreductase subunit H Paracoccus denitrificans PD1222 0.038861152 1 LEVO MAEFWASPYGFALSMLLQGLAVIAFVMGSLIFMVYGDRKIWAAVQMRRGPNVVGPWGLLQTFADALKYIVKEIVIPAGAD KFVYFLAPFLSMMLALFAFVVIPFDEGWVMANINVGILFIFAASSLEVYGVIMGGWASNSKYPFLASLRSAAQMISYEVS LGLIIIGIIISTGSMNLTAIVEAQRGDYGLLNWYWLPHLPMVVLFFVSALAECNRPPFDLVEAESELVAGFMTEYSSTPY LLFMAGEYIAMYLMCALLSLLFFGGWLSPVPFIADGWWWMVIKMWFWFYMFAMVKAIVPRYRYDQLMRIGWKVFLPLSLG WVVLVAILARYEILGGFWARFAVGG A1B487 NADH-quinone oxidoreductase subunit F Paracoccus denitrificans PD1222 0.047281141 1 LEVO MLNDQDRIFTNLYGMGDRSLAGAKKRGHWDGTAAIIQRGRDKIIDEMKASGLRGRGGAGFPTGMKWSFMPKESDGRPSYL VINADESEPATCKDREIMRHDPHTLIEGALIASFAMGAHAAYIYIRGEFIREREALQAAIDECYDAGLLGRNAAGSGWDF DLYLHHGAGAYICGEETALLESLEGKKGMPRMKPPFPAGAGLYGCPTTVNNVESIAVVPTILRRGAEWFASFGRPNNAGV KLFGLTGHVNTPCVVEEAMSIPMRELIEKHGGGIRGGWKNLKAVIPGGASCPVLTAEQCENAIMDYDGMRELRSSFGTAC MIVMDQSTDVVKAIWRLSKFFKHESCGQCTPCREGTGWMMRVMERLVRGDAEVEEIDMLFDVTKQVEGHTICALGDAAAW PIQGLIRNFREEIEDRIKAKRTGRMGAMAAE A1B491 NADH-quinone oxidoreductase subunit D Paracoccus denitrificans PD1222 0.046811483999999993 1 LEVO MDGDIRKNSYDDGSMDALTGEQSIRNFNINFGPQHPAAHGVLRMVLELDGEIVERADPHIGLLH(2MR)GTEKLMESRTY LQNLPYLDRLDYVAPMNQEHAWCLAIERLTGTVIPRRASLIRVLYSEIGRILNHLMGVTTGAMDVGALTPPLWGFEAREE LMIFYERACGARLHAAYFRPGGVHQDLPPDLLDDIEEWCERFPKLVDDLDTLLTENRIFKQRLVDIGIVTEADALDWGYT GVMVRGSGLAWDLRRSQPYECYDEFDFQIPVGRNGDCYDRYLCRMAEMRESCKIMQQAVQKLRAEPAGDVLARGKLTPPR RAEMKRDMESLIHHFKLYTEGFKVPAGEVYAAVEAPKGEFGVYLVADGTNKPWRAKLRAPGFAHLQSIDWMSRGHMLADV PAIIATLDIVFGEVDR A1B495 NADH:ubiquinone oxidoreductase 17.2 kD subunit Paracoccus denitrificans PD1222 0.014432875 1 LEVO MSFLLRFLTWWNSQTLNTQVWTKLYGEKVGEDDQGNVYYQSGGGKRRWVIYNGESEASRISPEWHGWLHHTYKEPPTAAP LAHKPWEKPHEPNLTGSSGAYHPAGSLYRAQPVERRDYDAWQPE A1B1H8 NADH-quinone oxidoreductase subunit A Paracoccus denitrificans PD1222 0.013686093 1 LEVO (FME)EYLLQEYLPILVFLGMASALAIVLILAAAVIAVRNPDPEKVSAYECGFNAFDDARMKFDVRFYLVSILFIIFDLE VAFLFPWAVSFASLSDVAFWGMMVFLAVLTVGFAYEWKKGALEWA A1B498 NADH-quinone oxidoreductase chain 10 Paracoccus denitrificans PD1222 0.021835205 1 LEVO MMTFAFYLFAISACVAGFMVVIGRNPVHSVLWLILAFLSAAGLFVLQGAEFVAMLLVVVYVGAVAVLFLFVVMMLDVDFA ELKGELARYLPLALVIGVVLLAQLGIAFSGWTPSDQAESLRAAPVDAAVENTLGLGLVLYDRYVLMFQLAGLVLLVAMIG AIVLTMRHRKDVKRQNVLEQMWRDPAKTMELKDVKPGQGL P29922 Zinc finger CHCC-type domain-containing protein Paracoccus denitrificans PD1222 0.007069930999999999 1 LEVO MTIPAPEIQTVTSWKVACDGDEARGLGHPRVWLAIPRDTGWVECGYCDKRFVIDREHAHDDH A1B357 ETC complex I subunit conserved region Paracoccus denitrificans PD1222 0.012048399 1 LEVO MRVRIYKPARNAMQSGTARTRNWVLDFPPADPRAIDPLMGWTSSDDTQSQVRLRFETRKQAEDYAREHGLDYEVIEPHTR AANIRPRGYGENFASDRRAPWTH A1B1M0 NADH-quinone oxidoreductase subunit C Paracoccus denitrificans PD1222 0.023920102 1 LEVO MSEALSDEALLELAEHIALRRENDVISTQVAFGELTVNATLSGVIGLIEFLRNDPNCRFSTLIDITAVDNPARPARFDVV YHLLSMYQNQRIRVKVQVREDELVPSLIGVFPGANWYEREVFDLFGILFSGHSDLRRILTDYGFRGHPLRKDFPTTGYVE VRWSDIEKRVVYEPVNLVQEYRQFDFLSPWEGAKYVLPGDEKAPEAKK A1B496 NADH-quinone oxidoreductase subunit B Paracoccus denitrificans PD1222 0.019525543 1 LEVO MMTGLNTAGADRDLATAELNRELQDKGFLLTTTEDIINWARNGSLHWMTFGLACCAVEMMQTSMPRYDLERFGTAPRASP RQSDLMIVAGTLTNKMAPALRKVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGI LQLQRRIRRTGTLVR A1B497 NADH dehydrogenase subunit L Paracoccus denitrificans PD1222 0.077811352 1 LEVO MEKFVLFAPLIASLIAGLGWRAIGEKAAQYLTTGVLFLSCLISWYLFLSFDGVPRHIPVLDWVVTGDFHAEWAIRLDRLT AIMLIVVTTVSALVHMYSLGYMAHDDNWTHDEHYKARFFAYLSFFTFAMLMLVTADNLLQMFFGWEGVGVASYLLIGFYY KKASANAAAMKAFIVNRVGDFGFLLGIFGIYWLTGSVQFDEIFRQVPQLAQTEMHFLWRDWNAANLLGFLLFVGAMGKSA QLLLHTWLPDAMEGPTPVSALIHAATMVTAGVFLVCRMSPLYEFAPDAKNFIVIIGATTAFFAATVGLVQNDIKRVIAYS TCSQLGYMFVAAGVGVYSAAMFHLLTHAFFKAMLFLGAGSVIHAMHHEQDMRNYGGLRKKIPLTFWAMMIGTFAITGVGI PLTHLGFAGFLSKDAIIESAYAGSGYAFWLLVIAACFTSFYSWRLIFLTFYGKPRGDHHAHDHAHESPPVMTIPLGVLAI GAVFAGMVWYGPFFGDHHKVTEYFHIAGAHHEAAEGEEAEHATAEAPVEHAVADTATAEGEAAAEAEHAEIAAPVGGAIY MHPDNHIMDEAHHAPAWVKVSPFVAMVLGLITAWTFYIANPSLPRRLAAQQPALYRFLLNKWYFDEIYEFIFVRPAKWLG RVLWKGGDGAVIDGTINGVAMGLIPRLTRAAVRVQSGYLFHYAFAMVLGIVGLLIWVMMRGAH A1B481 NADH dehydrogenase subunit M Paracoccus denitrificans PD1222 0.056519906 1 LEVO MTNLLSIITFLPIVAAIIMALFLRGQDEAAARNAKWLALLTTTATFVISLFVLFRFDPANTGFQFVEDHAWIMGLRYKMG VDGISVLFVLLTTFMMPLTILSTWQVQDKVKEYMIAFLVLEGLMIGVFTALDLVLFYLFFEAGLIPMFLIIGIWGGKDRI YASFKFFLYTFLGSVLMLVAMIAMYRMAGTTDIPTLLTFDFPSENFRLLGMTVVGGMQMLLFLAFFASFAVKMPMWPVHT WLPDAHVQAPTAGSVLLAAVLLKMGGYGFLRFSLPMFPVASGVAQPYVFWLSAIAIVYTSLVALAQSDMKKVIAYSSVAH MGYVTMGVFAANQIGVDGAIFQMLSHGFISGALFLCVGVIYDRMHTREIDAYGGLVNRMPAYAAVFMFFTMANVGLPGTS GFVGEFLTLMGVFRVDTWVALVATSGVILSAAYALWLYRRVTLGQLIKESLKSITDMTPRERWVFIPLIAMTLILGVYPR LVTDVTGPAVAALVQDYNQSQPAAPVATAQASH A1B480 IRON/SULFUR CLUSTER 0.00035163999999999996 6 SF4 FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES SODIUM ION 2.299e-05 1 NA 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 0.000704998 17 3PH O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine 0.000792075 2 P5S CALCIUM ION 4.0078e-05 4 CA 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 10 3PE CARDIOLIPIN 0.0014640429999999997 2 CDL FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 2 PC1 ZINC ION 6.5409e-05 1 ZN UBIQUINONE-10 0.0008633429999999999 1 U10 water 1.8015e-05 1080 HOH singleParticle particle 2.0 6.5 UltrAuFoil R0./1 GOLD GLOW DISCHARGE AIR
The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for two days under anaerobic conditions. The grids were then washed in 100% ethanol and dried three times prior to sample application.
 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 2.4 81000.0 NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 3 16814 2.4 40.0 1 CTFFIND 4.0 PHASE FLIPPING AND AMPLITUDE CORRECTION BACK PROJECTION 2.3 FSC 0.143 CUT-OFF RELION 3.1.0 146603 PROJECTION MATCHING MAXIMUM LIKELIHOOD RELION 3.1.0 4 RELION 3.1.0 emd_18324.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 476.8 476.8 476.8 90.0 90.0 90.0 X Y Z -0.043334004 0.11134344 -0.00014545044 0.002713615 0.745 0.745 0.745 0.019 AUTHOR Globally sharpened consensus map Other in silico model
Model Angelo
 AB INITIO MODEL REAL emd_18324_msk_1.map emd_18324_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 476.8 476.8 476.8 90.0 90.0 90.0 X Y Z -0.014662393 0.06350727 -0.0001450051 0.0014895415 0.745 0.745 0.745 AUTHOR Half-map 1 emd_18324_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 476.8 476.8 476.8 90.0 90.0 90.0 X Y Z -0.013643208 0.06529064 -0.00014589577 0.0014928331 0.745 0.745 0.745 AUTHOR Half-map 2