2025-12-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY database_2 em_3d_fitting_list em_admin entity pdbx_initial_refinement_model _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 _entity.pdbx_description EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin entity pdbx_entity_nonpoly pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 _entity.pdbx_description _pdbx_entity_nonpoly.name _pdbx_entry_details.has_protein_modification STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_admin.last_update _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id DATA_COLLECTION em_admin _em_admin.last_update PDBe PDBe 2020-04-02 2020-08-12 2020-08-12 2025-12-17 Medical Research Council (MRC, United Kingdom) MC_U105663141 United Kingdom Medical Research Council (MRC, United Kingdom) MC_UU_00015/2 United Kingdom Hirst J Grba D NADH:Ubiquinone Oxidoreductase, complex I, MEMBRANE PROTEIN Grba DN Hirst J Nat.Struct.Mol.Biol. US 27 892 900 2020 32747785 doi:10.1038/s41594-020-0473-x 1545-9985 Grba DN Hirst J Nat.Struct.Mol.Biol. US 27 892 900 2020 32747785 doi:10.1038/s41594-020-0473-x 1545-9985 6yj4 FULLOVERLAP EMDB EMD-10815 associated EM volume

High-resolution cryo-EM structure of mitochondrial complex I reveals ordered water molecules for catalysis and proton translocation

Yarrowia lipolytica mitochondrial complex I (NADH:Ubiquinone oxidoreductase) Yarrowia lipolytica mitochondrial complex I (NADH:Ubiquinone oxidoreductase) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 Yarrowia lipolytica mitochondrial complex I 1 1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 Yarrowia lipolytica Entity 10 1 10 Yarrowia lipolytica (strain CLIB 122 / E 150) NADH-ubiquinone oxidoreductase chain 3 Yarrowia lipolytica 0.014506339 1 Yarrowia lipolytica LEVO (FME)NTFIIFIILIPIVGFALLAVNILLAVYKPYNEKLGAFECGLTSFNQTRLAFNAAFILVAILFLPFDLEISTLLPY VMSIYLVSNYGFTIVLLFLLILIIGFVYEINTNALKINKHNKPNTDSLIYKL S5TMS4 7.1.1.2 Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.023455175999999998 1 Yarrowia lipolytica LEVO MLRSQIGRLALRPTLVPATVIPQTRAYSAPAGTPRVSSSSMPTDFPLPSQQKPNSAVDYTLTTLDAVANWARQGSFWPVT FGLACCAVEMMHVSAPRYDQDRLGIIFRASPRQSDIMIVAGTLTNKMAPVLRQVYDQMPEPRWVISMGSCANGGGYYHFS YSVVRGCDRIVPVDVYVPGCPPTSEALMYGVFQLQRKMRNTKITRMWYRK Q9UUT7 1.6.99.3 NUGM protein Yarrowia lipolytica 0.03364491 1 Yarrowia lipolytica LEVO MLSRFARIGSMGIRPVAAARATFVTSARAAQAAPSWENIKDIRLDPKVHVDEVYEPIVNPADRYLQHVSDLHQYAKYIMA ALPKYIQGFSVWKDELTLHVAPSAVIPVTTFLRDNTSTQYKSIIDITAVDYPSRENRFEVVYNFLSVRHNSRIRLKTYAT EVTPVPSITCLYEGANWFEREAYDMYGVFFEGHPDLRRIMTDYGFEGHPLRKDFPLTGYTEVRWDEEKRRVVYEPLELTQ AFRNFSAGSTAWEPVGPGRDDRPDSFKLPTPKPEEKEGDKKAAAAAAHHHHHH Q9UUU0 1.6.99.3 NUCM protein Yarrowia lipolytica 0.052521949 1 Yarrowia lipolytica LEVO MLRSAAARAVRAVRPRLSARYMATTALPQDPIPSGALGQKVPHVDESHQDLLFRTSHMVEDLETYDEDSPINTSDANTRI RAFTINFGPQHPAAHGVLRLILELSGEEIIRSDPHVGLLH(2MR)GTEKLIEYKTYMQALPYFDRLDYVSMMTNEQVFSL AVEKLLNVEVPLRGKYIRTMFGEITRVLNHLMSVCSHAMDVGALTPFLWGFEEREKLMEFYERVSGARLHAAYVRPGGVS QDLPAGLLDDIYMWATQFGDRLDEIEELLTDNRIWKLRTVNIGTVTAQDALNLGLSGPMLRGSGIPFDIRKNAPYDAYDK VDFDVPVGMNGDCYDRYLIRMAEFRQSLRIIEQCCNDMPAGAVKVEDFKINSPPRNLMKEDMEALIHHFLLYTKGYSVPP GETYTAIEAPKGEMGVYVVSDGSERPYKCKIRAPGFAHLGAFDHIARGHFLPDAVAIIGTMDLVFGEVDR Q9UUU1 1.6.99.3 Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.027247401999999997 1 Yarrowia lipolytica LEVO MLRLIRPRLAALARPTTRAPQALNARTHIVSVHRNTENNNPSIPFEFSPENMKRAEEVIAKYPPQYKKAAVMPLLDIGQR QLGYTSISVMNYVAKLLEMPPMRVYEVATFYTMYNRTPMGRYHLQICTTTPCQLCGSDGIMEAVQNTLNIKPGETTKDNL FTLSEVECLGACVNAPMMAINDDYYEDLTPEGTVKLLEDCKAGKMPTPGPENHVRRDCEPASGQKVLLSKEPHNVADFLQ EGI Q9UUT9 1.6.99.3 Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.053829508 1 Yarrowia lipolytica LEVO MLRTTLHKRGLARLSRGFATTQDATPKARQYGGLKDQDRIFQNLYDNYGWDLASARKQGDWYKTKELILKGDTWIIDEIK KSGLRGRGGAGFPSGLKWSFMNPPGWEKNEGPRYLVVNADEGEPGTCKDREIMRKDPHKLVEGCLLAGRAMNATAAYIYI RGEFYNEAAVLQTAINEAYAAGLIGKDACGSGYDFDVYIHRGMGAYVCGEETSLIESLEGKAGKPRLKPPFPAGVGLFGR PSTVTNVETVAVAPTILRRGGDWFASFGRERNSGTKLFCISGNVNEPCTVEEEMSIPLRELLEKHCGGIKGGWDNLLGVI PGGCSVPILPKNICEDVLMDFDALKDVQSGLGTAAVIVINKQQDVIRAIQRFAAFYKHESCGQCTPCREGTTWLLKAMDR FRTGQAKEREIDMLYELTKDIEGHTICALGDAAAWPIQGLIRNFRPEMETRMKKFHDEVGAVSVGGWMKDARVEKGKVVG APLPGVHH Q9UUU2 1.6.99.3 Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.07908807799999999 1 Yarrowia lipolytica LEVO MLSRNLSKFARAGLIRPATTSTHTRLFSVSARRLAEIELTIDGHKVSIEAGSALIQACEKAGVTVPRYCYHDKLAIAGNC RMCLVDVERAPKPVASCAYPVAPGMVVRTDTERVKQARENVMEMMLQNHPLDCPVCDQGGECDLQDQSMRYGRDRGRFTE ITGKRSTEDKNIGPLVKTSMNRCIHCTRCVRFANDIAGAPELGSSGRGNDMQIGTYLEKNLNTELSGNVIDLCPVGALTN KPYAFRARPWELKKTESIDVMDAVGSNIRIDSKGVEVMRVIPRVHEDVNEEWINDKSRFACDGLKTQRLTTPLIRVGDKF VNATWDDALSTIAKAYQQKAPKGDEFKAVAGALVEVESMVALKDMTNALGSENTTTDTPNGNSAPAHGITFRSNYLFNSS IAGIEDADAILLVGTNPRREAAVMNARIRKAWLRQELEIASVGPTLDATFDVAELGNTHADLEKALSGEFGEVLKNAKNP LIIVGSGITDREDAGAFFNTIGKFVESTPSVLNENWNGYNVLQRSASRAGAYDIGFTPSDEASKTTPKMVWLLGADEVAA SDIPADAFVVYQGHNGDVGAQFADVVLPGAAYTEKAGTYVNTEGRSQISRAATGPPGGAREDWKILRAVSEYLGVALPYE DAYEVRDRLAEISPSLVRYDLVEPTVFGDVAVQHSLVGPNGSVTPSSAPLTETIENFYMTDSISRSSPTMAKSSIAFNKD NKKNQAFA Q9UUU3 1.6.99.3 NADH-ubiquinone oxidoreductase chain 1 Yarrowia lipolytica 0.038389277 1 Yarrowia lipolytica LEVO (FME)IINIVEILIFLVCVLFSVAYLTVAERKTLAYMQRRLGPNFVGYYGLLQAFADAVKLLLKEIVLPKESNYIILVIS PLITLITALIGWVVIPLGPGITLGELNLGILFSLAIGSLGVFGSLLSGWSSNSKYSLLGSIRSTAQLISYELILTSIFII IIMFVSSLNITTIIETQRVVWYCIPLLPLLLIFFIASVAETARPPFDLTESESELVAGYFTEYSGSPFVFFFLAEYSNII LISAFNGYLLLGGYLSFNYSYLFNILFNDYSYVSFLFEGLINSSAYAIKLVFLMFSFIWVRAAFPRFTYDNLINFCWIIL LPLLFGIFLIIPSTLYIFDSFPTLI S5U3V2 7.1.1.2 Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.025682305 1 Yarrowia lipolytica LEVO MLSLVRPAVTRSILRGAPGSMRLLSSTARLHAPATDSAINIYAGGSAAAAPPAGFRIHRPATWEESEEGALSKATKYFLL AEMFRGLYVVLEQFFRAPYTIYYPFEKGPVSPRFRGEHALRRYPSGEERCIACKLCEAICPALAITIDAEERIDGSRRTT KYDIDMTKCIYCGYCQESCPVDAIVETPNVEYATETREELLYNKEKLLANGDKWELELQYALDADAPYR Q9UUT8 1.6.99.3 NADH-ubiquinone oxidoreductase chain 6 Yarrowia lipolytica (strain CLIB 122 / E 150) 0.020793111 1 Yarrowia lipolytica LEVO (FME)MYLTYYFIEITIFLAILCTIFIISAKNPMVSILYMIALFVIAAMYLYLIGLGIFSLLYIMIYIGAIAVLFLFIIT LLDINSTELSVKSNIRDLPLVLISLIVLTISGLMIYSNDSILINKLLEAFGNDYNTIITQDWFNIENTTLLTTIGNVLLT NNAFILLVLAIVLLLGIIGPISITMKHKE Q9B6E9 7.1.1.2 NADH-ubiquinone oxidoreductase chain 4L Yarrowia lipolytica 0.00984386 1 Yarrowia lipolytica LEVO (FME)FIGTIILVLSFLGFVFNRRNIILAFICLETMLLGINLILLRNSVLFDDISGSLFAIVIIILAGVESAIGLSLLVS YYRLRGVINSYGI S5U4U1 7.1.1.2 NADH-ubiquinone oxidoreductase chain 5 Yarrowia lipolytica 0.07376870299999999 1 Yarrowia lipolytica LEVO (FME)YNAISLIIILPCISWLFPLFFGRQLGYVFVTRMTSTLIIITTLITYYYFYQLLGNNNPINLELFNYLNIDYLDIN YNFEIDALTITMLLAITTISSMVHIYSIGYMETDPHQVRFFSLLSMFTFWMIILVTGSNYFVLFVGWEFIGVTSYLLISF WVTRLQAMKSALSAVLMNRFGDAFFVLGLCVIAYVFGTLNYSTIFATAYLINTDLLVLIMLALFIAAMAKSAQFGLHNWL TLAMEGPTPVSSLLHAATLVTAGIYLLLRSANILEYTPTVLFIILWIGALTTLSAGLIAICSNDLKRIIALSTMSQLGMM TIAIGLSAYNLALFHLLGHAFFKALLFMSAGSIIHSILNESQDIRTYGGLLSYLPYTYICITIASLSLMAMPGLTGYYTK DIIIESTYGSYSISNYVVYWIAYLSAVLTCVYSMKILYLTFYSNPNNNTITYYNAHESNIYITLPMFILAIFAMFAGWIL KDIYLGVGTDFVGTHILPNNFSYFDTEFSITQFYKLLPLISAILVSILIVVLNEFFAIVFNLNNKYINTVYSIFNQKLVS DQILNHFIIFKGLVTSGNIAHHVDKGSLYRLGPVGINRLLNKASYNVINLSSNTRSSLSMNSMLILITIVSLLLLVLVMN VNFIIVIPVLISILYILFS S5TF58 7.1.1.2 NADH-ubiquinone oxidoreductase chain 4 Yarrowia lipolytica 0.054534651999999996 1 Yarrowia lipolytica LEVO (FME)FLTSILLSSLYLFNRILAWQGNVKHFYLFASNLLLLFIVVLYINFNTFSNSFQFNFELFNSLNPFGLSNSDISNG LLFGIDGLSLTFILLTVLLIPLTLLGNWYNINFNSNLYYTLVLAIGLVILLNFWALDYISFYILFEATLPLLFILIHIYG SSDSERASFYVLMFTLSGSLFMLLSIVVISIVLNTTNFINHNLFVLSLDLQTIIWLGLFIAIMVKTPLFPIHVWLPVVHS ESPLAGSMILAGLILKLALYAILRLLLPLLCEAQILYTPMIYIISLLTIILTSLATLRQIDLKVIIAYSSISHMGIAILG VCSNTSLGIYGSIVLGVAHGFVSPALFLIVGGILYDRYHIRIVNYYKGLTTYMPQLATYIIILSFANIGTPLTGNFTGEF LSLQGGFIRNPIIGGISCISVLLAAIYQLKLTNKLTGGISSIYMHRTNDVTIREKFIMNILIISTLIIGICPQIMYNLLY WTVNNYIYII S5TMP9 7.1.1.2 NADH dehydrogenase subunit 2 Yarrowia lipolytica 0.053381367 1 Yarrowia lipolytica LEVO (FME)LILAIISLITFVSMSKLSDNRAIIRLINIYLILVLVLDSFLYLLFLNNQTYTVMGELLIFNSFTFYIDMLIYFIM IVISSLYGYNLYNNNLYKTLFEPKKELIILFLINILGALLIVHSNDFITLFVAIELQSYSIYLITAIYNSSYKASKASML YFFMGGILSILIAYSINTYYSVLNSYTLHSLDSLIINTLDLNLILIALSLGLLFKIGIAPLHKWLISIYENTPILITIYI SLIPKISILSYLVLSNISINSLVISILAILTLLVGSVGGLLQIKIKRLLAFSGLTNAGYMMLLLLLNNNEFSYLYYITQY SISHLAIFMIIIFSIYYINYINNQYNPIIYVNQLKGLIHDNAYLVLSMAIVVFSFIGIPPLLGFFGKLNILMSILNNGYY FISIVLIVASLISALYYLYLLNVSIQDKNNILINSNETVSSVLSYILSSLIILITFGFIYNSLIIDIFNVYFN S5U4R9 1.6.5.3 Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.018588208999999998 1 Yarrowia lipolytica LEVO MSSSTPLVKTSVNYSYGDYPLIDADPHFKRVVGYMRPSDYGVIGLATAALPAGICFAEWLDPVKGKFARPSVKFLRVATM LGFAVGFGAAYARSSLRFFGVTENAREYKKDEAQMAARKAAGLEPYGTSSLTPELQEIAAKNSAHSIAGLFIFPWFNFVN HPYHGREQK A0A1D8NKB4 Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.042765738 1 Yarrowia lipolytica LEVO MLRTTRAVKPLKAITTSVRFMNSFENLAQDVNITRSGKTLIAKGTGGRSSRTGYTATVFGANGFLGSYLTAKLAKHGTTV VVPYREEMAKRHLKVTGDLGVVNFLEMDLRNLESIDEAVRHSDIVVNLIGREYETKNFNYYDVHVEGARRIAEAVKKHNI ARYIHVSAFNAEIDSPSEFNHTKGLGEQVTKDIVPWATIVRPAPMFGREDKWFLDRMARSPCLVSANKFQETSNPVHVID VAAALERICFDDSTVAQTFELYGPQKFTQKQIIDMVSETLRKEVRHIELPKALYQAYTKATQAIWWPTYSPDQVERQFLS QKIDPSAKTFNDLDLTPMELPDLMFKLIRPYRVNTFQHDVSQLENKEKTFVHILD A0A371BY45 Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.018656080000000002 1 Yarrowia lipolytica LEVO MLSRSLRQLSQPSVRSFATSARLLQKKDVPEVGVNLDNVPAHEIVSGAPAELSRNRVVRIYQQAKPATQSGEYGTFAWRL DWDIVDVANRWENDLIGWQSSGDYMQATQMKFTSKESAIKFANKQGWDFYIQEPHHRKFRVKQYANNFVHSYGKLKHIRT K A0A1D8N7X0 Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.01514897 1 Yarrowia lipolytica LEVO MLSRFVSKRAFSVSTQVSKSIISYNGNTIEIPEEYTKQAPNRDSTWAPAQASKTEIYKNNMVRFEQKDLSKQPMPYAGIE LIAQQPVRFVHGNTAVCDGANHNGPGAQGHPKIFINVDAPGSHACQYCGTRYEKEH A0A1H6Q8Z5 Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.009621050999999999 1 Yarrowia lipolytica LEVO MSAALREIRFHLCQNGSSSAPLRQFVKNQIGAFQKANPSTKVLVREANGVKPIVFARFDHGHESKIGLDVSSEKEVAERV KSLIEAK A0A1H6PJS3 Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.012053584999999999 1 Yarrowia lipolytica LEVO MLRNVSRLALRSNFARQATMGQRFYSVARPDAEKRIAAVLESFDKISNPAAITPTASFAKDLNLDSLDTVEVVVAIEEEF GIEIPDKEADEIKSVNQAVEYILAQPDAK A0A1H6PXT9 Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.014444458 1 Yarrowia lipolytica LEVO MLRQSVLRLSRAAVARPALSRSFVTAVARPQLVRAAPVSFIRHYSSAHVLTKDMIQERIVALLESFDKVNDAKNITATAN LTSDLGLDSLDVVEVVMAIEEEFGLEIPDHDADEIKTVQQAIDYVSAQPAAV A0A1D8NG21 Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.016657919999999996 1 Yarrowia lipolytica LEVO MRYTQLLRNVSKGVQKSGQSVLVQMREGTPIGLTGIYQHPNPRPALIALYEATLKELQDKHPKDSVYRQSIENLTAHRKQ IVEDNEVSEVIENKIGAGLIEEVVIQAHEELELAKKMSEWKPWEELEEKPLEDQWVYFNKKGVE A0A371C5F3 Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.014778817999999999 1 Yarrowia lipolytica LEVO MAIIATAFAETVKFSGSKQELQKRTLALYRQFLRGAPTFADLYEVQFSIPTIRTKIRQEFERHRFVDDLSIQNVLYAKGH MEYQECINFWKQQAQFLKYFPEEDDIQGRHQPSNFVDKFLKNRA A0A1D8N3C8 Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.019355196999999998 1 Yarrowia lipolytica LEVO MPREAAAHWVPFEDKANMPDNVPDVVEVGATSAPLLSASYFIGAKCKPYNDDFMLCREESQGSGAIDCLKEGRRVTRCAV SVIEDINKSCLDEFRLHWQCLEQNNHQLSGCRKAEALLNKCVFTKLNLEKKIPGLRPDEEPVFLKKDPWIKPAVDDFKSV RAYAEAKKNGTL A0A371C2D0 Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.020849550999999997 1 Yarrowia lipolytica LEVO MSEHVHLPSPTFNTSSAGHFHPYNTLGLATQSAMVGLGAGVVAAAARNSLATGPRNILTTFSKSGGVVTIFTGASIAYVF TYCSAANLRERKDGWNHMWAGAATGAVLGARTKLVPAFIGWTVLCGAACGLFGWTGARFNADRKASLEQSPKGFVQEDAH QTFWEVVHRRPLSLTVEQLGEGRGINAVPIATATEAPN A0A371CB65 Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.014112429 1 Yarrowia lipolytica LEVO MPSVGQDLPPVGGYEPVQWRRNLPARGFRPLVYLAALCGICGYGFYRALGGIQERRELKREKLWARIYLMPLLQAEEDRQ TVRRSIAQLEREKEIMKGTGFDVDKSVYNDGKFHAPALMIPPK A0A1H6PPE5 Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.009806237999999998 1 Yarrowia lipolytica LEVO MAIPFEALLPYGIIFGLLTAGGGAMQVLHVYRNGGVRDRFAIDQWDSQMMERDLRLNGGQGRKQVDQATAPEAFKHNHVW KSERPLI A0A1D8NC63 subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.008992229 1 Yarrowia lipolytica LEVO MINANPGFWNGPFRYLRWSAHNRPHLFFAFAIGIAGPVAALTLTPLRRKYLYPDHSPLPQSYPLPQRAREQLTGFDDE A0A1D8NJR0 Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.019772525 1 Yarrowia lipolytica LEVO MLPGGPVPVFKKYTVGSKGIWEKLRVLLAIAPNRSTGNPIVPLYRVPTPGSRPEANVYQDPSSYPTNDIAENPYWKRDHR RAYPQTAFFDQKTVTGLLELGSEATPRIADGEAGTKALANIANGGVSFTQALGKSSKDVIYGEVLTVNGLPPVAPTLAPK QWKIIEGEAAIYPKGYPCRTFH A0A1D8N3H5 Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.008059366 1 Yarrowia lipolytica LEVO MALFTSLVGASGLGFATKFLSNKIRLKPAGYYPLGYVFSGVAWAGLGLVLHNVHQHSLEVLEKKKTALSEQRTE A0A1D8NGI5 Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.010035651 1 Yarrowia lipolytica LEVO MTAAGISLTGGRNRCFSEWQSFMHCTAKTDAKSRAQCLPNFEDYMECLHHTKEKARLREIESVLKQKKEGLEAPPVKVIP VKAIGLVEE A0A1D8NNZ0 Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.016175141 1 Yarrowia lipolytica LEVO MSSSLYRVLRNAWEVGPRSYWKQLNSIGDTKSGRLVGTDIYGNKFYETDHQDEIHLRTRYVEYKEKDYDMSQVEPGWHFW LGYGVDTAPCNTPKEKLPIRAYPYKFQPNYTGTPGAFVTYNTLKPKISAWEPVTKQRS A0A1D8N5V2 Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.028479940999999998 1 Yarrowia lipolytica LEVO MLKLHYRNFITAQHSTTNTTPTMIASVCKRAGLRAGPRAYPGVRQFALRAYNEEKELALKQRLSQLPPPGKAFVTAEGEP RPAKEAELAELAEIAALYKTDRVGILDILLLGNKHARLYRDNTALLKDYYYNGRRILDKIPVKDKQTGKVTWEIKREGAE KEDWVNQMYFLYAPSLILLLIVMVYKSREDITFWAKKELDQRVLDKHPEINDAPENERDALIVERIIAGDYDKLASLQKK ATPTPATLI Q6ZY23 1.6.99.3 subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.015818789 1 Yarrowia lipolytica LEVO MLRHTVRATQTLRQARNVRFGSHGHGPELTPAVPFFQPYVLKWAGVSLGLVAFYQFNSSYEAKNGHTWVETFFHPKSRED ILNEEAKIVQALNNQRELTIKMHELKREEKDYAHSYSPLFSDPVPQGGSIGKAPGSSRE A0A371CFV9 Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.009793966 1 Yarrowia lipolytica LEVO MGGGRYPFPKDVISMTGGWWANPSNWKLNGLFATGIAVGLALWVSTATLPYTRRREGITSESDISKWNAAAGVWRERHGK ISTGEAAESE A0A1H6Q311 subunit NIGM of protein NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.01076543 1 Yarrowia lipolytica LEVO MHNSSSVHHHYISKTTGFFRFRYKMAGHHTNYKWNGPLPRPHVSAGHRIATKFLGATMFFWMFLRIKEEYPAMLGLHNFY PPKEGEKAVEH A0A1D8NFX6 Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.006948902 1 Yarrowia lipolytica LEVO MAPQLKDPWARREAWRYQTNFTRANRFKGAAPGFGIAVVAFGAYLAAEKFLFEKKDDHHH A0A371C0F2 Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.017328523000000002 1 Yarrowia lipolytica LEVO MLSRRAVTMLRSPVARVAQVQVRGIRASFDKAEEPMLGDYPDIDPFPAQLKNPYKKYDDQQDRRNLEEPLSVNDDLYDMW SPDRFTHFKNQDALKYFIGFLTIFFGASYVATYFVPEKAAIPREFPYEGLWKESGGTEKSKAFFGQRSE A0A1D8ND94 Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.010494884999999999 1 Yarrowia lipolytica LEVO MVELKPSSAIQRGPLNKGGWDAPHALHNDGAIDRYAHWRTFYQERFKYTRATGKSTLIFLVAFPALIGYVAYQSEGLFEF AGKRRGESVTTRG Q6ZY24 1.6.99.3 Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.01290287 1 Yarrowia lipolytica LEVO MSHPVPFSAANKKLVTSMYRQSLKLARNWISNRQLFRQKAVEIRHKFDQNAQISNPRLLARTLDETRAHLYEFRHPDPIV PPSFPGGTKYERNVPPRMEKIMQHNLYEP A0A1D8NDL1 Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.011219027 1 Yarrowia lipolytica LEVO MAEFPPLLSQEDMKKHKILLAYRDRCAALLVPLNECRKKNYYMPWACGHERHEYEMCEVADFQRRVKAMDKLKAEKIEQA KAAAAAAAAAAAADAEESK A0A1H6PKH9 Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I) Yarrowia lipolytica 0.011039275999999999 1 Yarrowia lipolytica LEVO MSEHQRPELVSFDDINYNDHKKVREAQESYTREQFIRLEALKTVRKALEKCYEESGPNHFEDCKNLAEQYLDMLPTHRLQ GYLGYQRNDPSK A0A1D8N596 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 18 3PE IRON/SULFUR CLUSTER 0.00035163999999999996 6 SF4 DODECYL-BETA-D-MALTOSIDE 0.000510615 5 LMT DIUNDECYL PHOSPHATIDYL CHOLINE 0.000622834 8 PLC FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN CARDIOLIPIN 0.0014640429999999997 6 CDL NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 0.000745421 1 NDP ZINC ION 6.5409e-05 1 ZN ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate 0.000584703 2 EHZ water 1.8015e-05 275 HOH singleParticle particle 7.45 UltrAuFoil GOLD GOLD GLOW DISCHARGE 90

Gold grids pre-treated with PEG thiol reagent

ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 -1.5 -2.7 130000.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 2540 44.0 1 106302

Post manual curation of Relion auto-pick

RELION 3.1 Gctf PHASE FLIPPING AND AMPLITUDE CORRECTION

Low-pass filtered (60 angstroms) in-house map from previous work

C1 2.7 FSC 0.143 CUT-OFF RELION 3.1 49669 PROJECTION MATCHING RELION 3.1

Initial 2D classification to remove junk before the same in 3D classification.

MAXIMUM LIKELIHOOD RELION 3.1

Using Relion solvent-flattened 3D refinement

2 50000.0 RELION 3.1

One major good class isolated.

6G2J PDB experimental model emd_10815_msk_1.map emd_10815_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 474.74997 474.74997 474.74997 90.0 90.0 90.0 X Y Z -0.041052125 0.12825133 0.00003831578 0.0050448794 1.055 1.055 1.055 AUTHOR ::::EMDATABANK.org::::EMD-10815:::: Half map 1 emd_10815_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 474.74997 474.74997 474.74997 90.0 90.0 90.0 X Y Z -0.04058876 0.13036 -0.0000038112144 0.005046518 1.055 1.055 1.055 AUTHOR ::::EMDATABANK.org::::EMD-10815:::: Half map 2