2025-10-15 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-02-21 2025-10-15 2025-10-15 2025-10-15 Medical Research Council (MRC, United Kingdom) MC_UU_00015/2 United Kingdom Open state without NUQM and with flavoprotein (classification state 3) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs Grba DN Hirst J NADH:ubiquinone oxidoreductase nanodisc membrane protein complex, MEMBRANE PROTEIN Lee CS Grba DN Wright JJ Ivanov BS Hirst J Global conformations of Pichia pastoris complex I are distinguished by the binding of a unique interdomain bridging subunit. Sci Adv US 11 eadz0693 eadz0693 2025 41032597 doi:10.1126/sciadv.adz0693 2375-2548 9ihp FULLOVERLAP EMDB EMD-52876 associated EM volume
State 3 of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs
 Pichia Pastoris (Komagataella phaffi) mitochondrial complex I (NADH:ubiquinone oxidoreductase) Pichia Pastoris (Komagataella phaffi) 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 43 Komagataella pastoris 0.909 NADH-ubiquinone oxidoreductase chain 3 Komagataella pastoris 0.016019821 1 LEVO (FME)LQDLFNNYVILVGILGLIFLGVNYFIVESPRMDENNGNISDYIEKSGPFECGFSSFEQSHNPIPIAFILVALLFL PFDLEVSSMLPYIVSIYSVGIYGLIIFILFLLILIVGFIYEFNTKSLSITTILHKKNKALVKNLY E1UWC4 7.1.1.2 BA75_00622T0 Komagataella pastoris 0.023353986 1 LEVO MFVPCRTQISRSLAHSVRYASKQVATSHSYSSDLPTDIPVLSKRPHTNLLDYTFTTFDKMKNWARKSSFWPMTFGLACCA VEMMHVSAPRYDQDRLGIIFRASPRQSDIMIVAGTVTNKMAPALRQVYDQMPYPRWVISMGSCANGGGYYHYSYSVVRGV DRIVPVDIYVPGCPPTSEALMYGVFQLQKKMMDGQTHRMWYRSY E1UWB5 1.6.5.3 NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.03318368 1 LEVO MIAARSIQRAIGTKPLAVRAVVLTTNSFRGFSKSSMSRKADEEPLPVLRDLPRPEYGELHAPVYNPAEKYKEQIEELHKF GRYIMGCLPKFVQQFSVWKDELVIYVAPSALTQVATFLKDHTSAQFKACMDVTAADYPTRTNRFDVVYNLLSVRHNSRIR IKTYASEVSPVPSVVPLFQGANWFERETYDLFGIFFEGHPDLRRIMTDYGFQGHPLRKDFPTTGYTEVRYDAEKRRVVYE PLELTQAWRNFTVGSSVWEQVGDGKDFTPESFKLPTPAPDPEPEADKKK E1UWB1 1.6.5.3 NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.054962457 1 LEVO MFARLHAKRGWKSLARARVGSRFLSNSSIARAAQTKDNNDFYDVKTKKNDFFPVQVDGIESSLGKYEEFAKDAHEWESWN LQNEDHPEYPVKRTKIRHFTLNFGPQHPAAHGVLRLILELHGEEILRSDPHVGLLH(2MR)GTEKLIESKTYMQALPYFD RLDYVSMMTNEQVFSLAVEKLLNLEVPERGQYIRTLFGEITRVLNHLMSVLSHAMDVGALTPFLWGFEEREKLMEFYERV SGARLHSAYVRPGGVSQDLPAGLLDDIYMWATQFGDRLDETEELLTDSRIWKQRTIGIGEVTAEDALNYGLSGVMLRGSG VPFDIRKSQPYDAYDKVDFDIAVGTKGDCYDRYLIRMTEFRQSLRIIEQCCNQMPPGPVKVEDFKVAPPPRALMKEDMEA LIHHFLLYTKGYAVPAGETYTAIEAPKGEMAVYVVSDGSERPYRCKIRAPGFAHLGAFDHIARGHFLPDAVAIIGTMDLV FGEVDR E1UWA8 1.6.5.3 NUHM (24 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.027396690999999997 1 LEVO MSLLRLLPKATKPLQQRIVTVTPKRFSHMISVHRDTPKDNPEIPFEFTKENLERAKEIIAKYPPQYKKGAVMPLLDLGQR QLGFTSISVMNYVAKYLDMPPMRVYEVATFYTMYNRKPMGKYNVQVCTTTPCQLCGSDGIMKAITEHLQIRPGQTTPDNL FTLQEVECLGACVNAPMIAVNDDFYEDLTPERTVEILKGFQSGDIPKPGPADRHSCEPHSGPKVLTNETPYHVKDFIRDD L E1UWB2 1.6.5.3 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Komagataella pastoris 0.05223466 1 LEVO MLRQQVGRKLVSKRFFSGLKDSDRIFQNVYSKYGEDLKSSQQRGDWYKTKEIILKGHEWLINELKASGLRGRGGAGFPSG LKYSFMPPNPNREPQYLVVNADEGEPGTCKDREIIRKEPHKLVEGCLLAGRAMNATAAYIYIRGEFYNEAVALQTAINEA YKAGLLGKNACGSGYDFDVYIHRGMGAYICGEETALIESIEGKAGKPRLKPPFPAGVGLFGRPTTVTNVETVAVTPTIFR RSGAWFASFGRDRNQGTKLFCISGHVNEPCTVEESMSIPLKELLEKHCGGIKGGWDNLLGVVPGGSSVPIMPKHVCEDVL MDFDALKDVGSGLGTAAVIVLNKQTDIIRAIQRFSAFYKHESCGQCTPCREGTTYLQRMMDRFVTGQAKEKEIDLIYELS KEIEGHTICALGDAAAWPVQGLIKSFRPEMVERIKQYEAKLGESVSYGGWTSKGKVLDGKVVSNPIPHDAHHH E1UWA7 7.1.1.2 NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.079646414 1 LEVO MLSVKRSISRIPTARLFSTTRRQLKEVELTVDGVKVSIEAGSSIIQAAEKAGVTIPRYCYHEKLAVAGNCRMCLVEIERS PKLAASCAMPVQNGMSVLTNTPKIKKAREGVTEMLLENHPLDCPVCDQGGECDLQEQSLRYGSDRGRFHEIVGKRAVENK AIGPLIKTSMNRCIHCTRCVRFLNDVAGAPEFGTAGRGNDMQIGTYVERNVNSELSANVIDLCPVGALTSKPYAFRARPW ELKRTETIDVHDALGSNVRVDTRGIEVMRVLPRLNDEINEEWISDKTRFACDGLKTQRLTKPLIRQGNTFVDATWEEALA TIAEGFQKVQPKENEIKAIVGSLTDLESIVALKDLVNKLGSENVSTDGDATTVPPAHGADFRSNYIFNSTIDNIEEADQI LLVGTNPRHEAAVLNARIRKVWLRSDLEVHHVGEEFDSTFELNHLGSDVNALAKALTGEVGKKLSEASKPLIIIGSGVTE TQDAEAVYATVAKFVTSNANIVTPEWNGFNLLHREASRVGALDVGFTTQSPEVANTKAKFIYLLGADEIVNKDIPKDAFV VYQGHHGDLGASFADVILPGSAYTEKTATYVNTEGRVQSTRAATNPPGVAREDWMIIRALSEYLGATLPYDNLYEMRSRL ADVAPHLLRHEVVEPVSEGIAKVGFQSLVKPGIQSKGVLLKNPIENFYFTDVISKSSPTMAKCVGSFGSKIEKIKDEKAN SYLSFA E1UWA6 1.6.5.3 NADH-ubiquinone oxidoreductase chain 1 Komagataella pastoris 0.039698844 1 LEVO (FME)LNNLFDFIEYIEYWLIIVAFVASVLIVVAYLTVAERKTMGYMQRRLGPNAVGYYGVLMAVADALKLLSKEIVLPH NGDIIYVMSGPLISLFSVLLSWAVIPFGPGLSLLDSEYSIIYLLASGSIGVFGTVIVGWMSNSKYTVLATVRTTAQLISY ELVLTTVVFIIALIVSSLNINVIIESQYNIWYIIPFFPLCLIFFISALAETARPPFDNVEAESELVSGHMTELSASPFVI FFLSEYCSMVLMSTLTAIFFFGGYLPFSNTIHHLILNLFDQHSIYYFIIEGILLSGYLAIKANFFMFSFVWIRAAAPRLR YDLLILFCWYVLLPIVFAIVVFAPGILYCFDALPVII E1UWC2 7.1.1.2 NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.025544215 1 LEVO MFRPLALKPSCRAINRIPVCRFSTGLIAQKPTLALTSGSIQGTHPEGFRLPRPKTWEESSESALSKATKWYLLSEIFRGL YITLEMYFRAPYTIYYPFEKGPVSPRFRGEHALRRYPSGEERCIACKLCEAVCPAQAITIEAEERIDGSRRTYKYDIDMT KCIYCGYCQESCPVDAIVETPNVEYATETREELLYNKEKLLANGDKWEQEIQYALDADAPYR E1UWB3 1.6.5.3 NADH-ubiquinone oxidoreductase chain 6 Komagataella pastoris 0.018564352 1 LEVO (FME)NLEILDLSILGFYSLISSNSFESIAILVATIMPVITELWYNYSQLFALLYTLIYVGAVVILFVFILSVINEKEEY EYEYSGLFILILVLLLDDLDDNESNDNDYNNVYITDYADWFNNYNESDLSVIGNLLFTEYALLLLIISFILLMSIIGLIL IVKKD E1UWC7 7.1.1.2 NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.009118741 1 LEVO (FME)DLILLMLVAVGLNIIDIYIMIEILIMGCTVNTIYSASLDNDMIGLIYSLIQIIIAGVESAIGLSILVNYNRIRNS EEIENE E1UWB6 1.6.5.3 NADH-ubiquinone oxidoreductase chain 5 Komagataella pastoris 0.07243607 1 LEVO (FME)ILLCIFTPFLGSLISGFFGRYIGVNSSKWIVCLSIFVSVVSTYILFIDVIFNEIEYTYNIMNWLNVEYLVVDWSF TIDKLSVSMLVPVVTVSFLVHLYSVSYMSHDPHQQRFFSYLSMFTFAMIVLVTGDNYLILFVGWEFIGVASYLLISFWFT RFNAVKSGLSALLINRFGDALLVLGLSYLVLVTGSVNYNTVFALGSYLDVNMITVILICFLVASMAKSAQLGLHSWLLLA MEGPTPVSSLLHAACLVIAGVFLLMRSSPLLEYTPIVLLLILWLGGLSTLISGLIAMVSNDIKKIIALSTMSQVGIMMIA IGVSCYNLALFHLICHSFFKALLFMSAGSVIHSIISEYQDIRMYGGFRQFIPLAYTCIFIASLSLMAIPGLTGFYSKDII IESMYGEYTFSGFIIYWFALISATCTSLYSIRLIYYTFLNNPNSPKYIYINLKENDIVLITPMIILTILSIFGGYLLRDI YLGMGSPFNELFIHPNNLSLIETEFSLPSILKVLPLITGLGGGLILLLIYEFNYSLFLVYNNKNLSKLYSFFNQKIMFDQ LLNNLILRSGLNIGWLLNVHIDRGILQLFGPLGLWKLSTFISSKLNKLVFLNIGFILEIIVLSWLLIVFKVSLLKYILLL IIFIIL E1UWC6 7.1.1.2 NADH-ubiquinone oxidoreductase chain 4 Komagataella pastoris 0.054784211 1 LEVO (FME)LVQNLIIFNIIGIVLLVLLNNNNNGILNKKSLLTIKNELKLKQIGLIISIINILIIIENWIGFNSNYYGFQNIER FLNIYWGIDGISLLLVLLTLILGPIAILSNWKNLKGYYTYYVISINMLVILMALNFICLDLVSFYILFESTLAPLFLLIG IYGANNKNKAAYYVLIYTLASSLFMLLSIVIYYIIINSTDYIYINNIILSINLQSLLFIGIIIGIAVKTPLMPVHTWLPT VHSESPLGGSILLAGVILKLAIYGVIRLLLPNLSEISMMFTPIIYIISILTLIYSSLITLKQTDLKVIIAYSSISHLAVC MIGIFANNLIGINGSLILCLAHGFVSPALFILVGGILYDRYHNRLINYYQGLSTFMPIFSIYLVVFSFCNTGTPLSGNFV GEFLSITGAVIRHPIIGSLTAASVLLSACYQMKLTNRLTGSVFSQYLHITNDVTNREIFLLNWLLIPTIIIGIYPSFVTN ILNLASSTLIYSVLI E1UWC5 7.1.1.2 NADH-ubiquinone oxidoreductase chain 2 Komagataella pastoris 0.059097925999999995 1 LEVO (FME)LFTSLLLIIVYGSLVNKSHLLTKLINRLGLIIIIYTLLIHLNINTLENLSIGINMFNNLLLINSFNNTIIELILI ICILYVLLISFNITGLSIIDNLNYSKRTFIVIVLFNIIGLTLLPLVNDIMILFIIIELQSYSLYLLTAIFNESHNSTKSA LYYFIVGSIASFIILDATVSIYDDLGLTNIQYILMYIDKLEIFDLLCLLFGLFIKIGLAPFYSYSITIYSLSPTIITNYI SLMPKLSILTLIYIIMHYINIVNNTDLNYVISFLILISMFIGSFGGLNVIRIKTLLAYSSLLNVSYMLLAILSNSNESII AYIYYIIQYSLTHINIFSIILVISIYLPIMNNNITSNTVDNKYSNNGGNMLNVMITKYSPIEYINQLKNLFINNIFIAIA LCISIFSLIGIPPLTGFYGKYLVLISGLNNGYVLLSIVLIIASSISTVYYATILKVLSFDTLSFKDIISNNLIINTSPEN NNNEIKPEISNVISYVISSLTLIILLIIIQYENIVKGAYLVLLYNWV E1UWC3 7.1.1.2 NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.022263098000000002 1 LEVO (ACE)METYELIDSDPKFSRVVRYFRPSDYLTWALGTIGAPGLMVLFEKIEPAKGNTFKMPPPSIMRIATTIGFFGGFYY AYTSSTKRFWGYSENAKEVAKDRYEVKKALSEKKSPYGSSLLNPYQQDMSARNSTNSQLLLAIFPWFNVANHQSHGIDLR KYYEVRDGEENWNFTLPPLDQVKDLDVAQYKEYSNYP E1UWB9 1.6.5.3 NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.043349988 1 LEVO MFRQARFVSTFPLKSDINITKSGKTLLSVGQGGRSSRTGFTATVFGGTGFLGRVVVSKLAKHGTNVVVPFRNDRARRQLK VNGDLGVVNFVEFDIRNLKSIEDSVKYSDIVINLIGTEHFSKNFSIEDVNIGAAERIAKAAKEAGVSRLIHVSSYNANPS SSSDFYATKGIGEQVVRDNFGPDATIVRPAPMYFRNSPFLNELLQIKALGGNVIFKKEVYPVHALQVGEAIERIAFDDAT AGQTYELFGKERYSKKELREMIKHIIHIGQRGYYPYSAGFYLPAPEPFLYAFALIRQYISSQPRFNVDQLKRSHINQEID QSAKTFTDLGMVPDELSEYLYRYVKPHISYTSQTQNRTVYSKEDIEKLRDYVNTPNDSFNLFNV E1UWA9 1.6.5.3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Komagataella pastoris 0.018241705 1 LEVO MLRSLLKVQVRGFSCGRVVSAAKNTNITPAINEGHTDLAKELVSGAPKELITERVARIYQEAKAATQSGQHNTETWKIDW DILNKGNRWENDLMGYQSSSDYMQGTILKFDTREGAIRFAKGQGWDYYIQEPKVRRFVKKDYSANFYHSKGPLKHIRTK E1UWC0 NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.015717822 1 LEVO MLRLTRASIRRISTKELTTARIKDISKPDENNLQQQAPNRISPWSKSQKPRAEAQDNVRFAVKDLAKQPRPYAAIDLIYK QPIRYIEHDNVAVCDGNGGAQGHPKVYINLDQNKAIPCGYCGLRFAQAAFKEDIESSQN E1UWB7 1.6.5.3 NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.009858477999999999 1 LEVO (ACE)SSKFVFPKVVKELRFFLSQTGEASVPLRSFLTKTYPAIKKANPTLPILIREAYGIPPSVTARLEKGHEVKTNLEG FSADQIAKTLQSIA E1UWD3 1.6.5.3 Acyl carrier protein Komagataella pastoris 0.015507593999999998 1 LEVO MLRNVSRQLLRSSKVYLPQVAVVRTQTPAFVSPSIISKRFNITQSASTLTKEDVLTRSVSVLRGFEVKTKDIDLQTTFVQ DLGMDSLDLNDALVALEEEFDVVFDDKTANEIKTVGEVVDFVLANYLPTEQSINHTIR E1UWE2 Acyl carrier protein Komagataella pastoris 0.014780592 1 LEVO MNRFNHPILRTAFSKSKWNLSKYTSPLFRPSYARTMIPLRTYSSTPSLTKEIIYDRIVEILESYDNVKQGSTISPAASFS KDLGLDSLDTVEVLLELENEFSILIPDNEADEIKTVQQAVDYIAAQEDSI E1UWE3 NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.015590797 1 LEVO MRAFTYLRQAQEILIKANKGNPTGLTGLFQHPSPRPTLITLYKATLKNLEEKIPKESVYRTAVEAFTKERLSIVENNEII EDIEKKIGSGLVEELIVQANEEYDLIDKMAEWKAWEELEEKPLDDQWTYFGKKL E1UWB0 1.6.5.3 BA75_04796T0 Komagataella pastoris 0.014783013 1 LEVO MTNPTAFAQTTRYVKDSTEMRTLVLNLYRRYLRHSRGFVNNYNLDIPASQVRTKIRQEFERQRFVKDLPLKNVLYMKAQM EFQELVNFWKQQCHVMQYFESIDHQNKIKGDSFVQKFLKGAQ E1UWD6 1.6.5.3 NADH-ubiquinone oxidoreductase Komagataella pastoris 0.020718482 1 LEVO (ACE)SSTHTNDSLNSSNYVDKLKDTHFVFENDKLPSEIPDVEEVGATTAPLLSAAYFIGAKCQDYNDDFMLCQKEAKGN GPIDCLKEGRRVTRCASGVLKDLNTHCSDEFRLHWQCLSFSNLEYKNCRKAESLLNKCVFEKMNLVKKIPGIPEDRQIHL KQNPVLKPVALHQDSEVAFKKAQNENSI E1UWB8 NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.023507607 1 LEVO MSETTAEQTVVEQFHLPQPFWPTTKTKEGEYVPKDSIREASKVFIGSGVLLGGMHFRRLMQYKKGSARPGLAKYLNLFSL SKSQLIGFPVALGAFSFLSHSFANLQEGQTATGEFAASSIASLIGLSIFRTKKPLSSNVAIAVGMGSLFGFLTWAGNFNL GDNSYRAALEAGNGNEGGFDNKVIKTERQGFWEGVYRRPLSQTVEDLGEGRGIITQ E1UWB4 1.6.5.3 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Komagataella pastoris 0.017243695 1 LEVO (ACE)ATQDLPPISGYAPIQWKRNLPSRGFRPVIWFLGLCTATGYGFYQISLANREKIELKREKLWARAHLMPLLQAEQD RNVVRRTFAYYKREGEIMKDVPWWEVKSTYSNKDIFHPPQTVLFGKHIDRDSGLMYANSRNRFGPDEEETK E1UWD8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Komagataella pastoris 0.017446690999999997 1 LEVO MIPFEALIPYAIMFAGFCLGGGVMNSAITADITKRARGPNQEIKRNVGEDEGPRNYTKPRYNTDQWDKYFAVRDLRLTGS LRGQSDNAVAEESFKTNSIQPYSNTRRPWVLRRHIIMKNSPTKWARKYSSRRDEREQEIKDDYIRGMGEH E1UWD0 NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.009181521 1 LEVO MAIGDYPVYYKQPIRWLSYHAHTRPHVFYAIAVAALGPVFMMATPLRRKFLYDDHEPLPANGYPLPNRSRDKTLTGYDD E1UWD4 1.6.5.3 BA75_00589T0 Komagataella pastoris 0.020110991999999998 1 LEVO (ACE)SGGPVPVFKKYTTGSKGIWEKIRQLLTLVPNRSTGNPLVKNYRVPPPGSQTLKYKDPVTIPAGDIVKNQYYDRDH RRNYPRLVAFDQTKVSGLLTLGSAQNPRISVGEKGQKELAVFDQSVSLSSTLATIDPKVVKSELLAEGGSPVVAPSLNKK MKFRLTEESEHGMYPEDYPIRIFAQN E1UWC1 1.6.5.3 Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBM Komagataella pastoris 0.009050411 1 LEVO MIASLAGWGLFGVTVRAYQQGIRKVPFSYYPLGYVYSALGWVAFGYGFNLWTERNDKLLEKRVEKLKESRNLRLSKDD C4R4T8 BA75_05084T0 Komagataella pastoris 0.012251015999999998 1 LEVO MAPLQQVGRHGGPNKCFGEFQRVVECMTNAKHDSYEPCNNLKNDYLECRKHKVERYKAFLMQKHAEELGKDPEEIGAPFV RKRRFLTSKTLGLVDGDDYEIGVEKI E1UWD1 1.6.5.3 NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.00986431 1 LEVO MPYLVAFRPAVLVFFFIRQPIGAGLLAGGFLFWQADRHFNFGIRDNIHNFKQTILGFPTQASKWETFKQVDAQKRAQLVS GPSEEH E1UWE5 1.6.5.3 NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.027250256 1 LEVO MYPVIQSAARRLGVRCFSGTTSVRAFNLQLEKEIRSKIDSLPKLNNIFQNANGSVRQPSDTELQTIAELNSLVTNRKLSL TDYLFQNAANQALYVDNEADLKELDISSRQVVDKVPFKDAKTGEIKWKVVRENENEGWEKIMYVGFVPTMILIFAIVLFK DDKSIDEWAMDELLLRLKEKNLSDVELIDELDKLSKSHVGKIGASEINKRDAVIIERILNGEYDQLSGLKKKELPIIDL E1UWE1 1.6.5.3 NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.021224576 1 LEVO MLTRRSVGLLQSTRISPVLTNFSSSRFYSAHHESDKKHDDHHEEHHDEHHDDHHTPLGPAENIFNKWNVTPFVWLFATVG IFQWDKSHRESHDGKGILDFLGEIKVKESLDTYFKEYQTKVASTADLYGLISFTPKRDIHHYVIRVDEVPGKHFPTNTTG NFGNTVDFENLEPRRKPINPYL E1UWE4 1.6.5.3 NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.008335509 1 LEVO MSGHHIHTPSYIKPPTGGWNFTPANWKQNTVLVLVGFTACCVGLYKLGEAGSYNPKLKYKEEELSRWNQSAKKN E1UWE6 1.6.5.3 Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.007071343999999999 1 LEVO MSAHHAFKYVRGAIVPKPKVHPGYVITSKFLGGLMWFWIFYRAKQDYPVWFGLKHPWEH A0A1G4KQ11 NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.007141992 1 LEVO MAGNPWKRRDAWRSQGAFTRANRFRGALPGFFWGLGAFGVYCVYEKVFLTNDHHGHHEEHH E1UWD5 1.6.5.3 NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.017944210999999998 1 LEVO MLRQAYRLAGKTNSITSSSVFIRNKSFLPHFIPKNYSYGDYPRLKPENLQKRDPYLKYDDQANKRNFNEPLHPQQDDLDM WAPDHFDFVQDSIALKWFGTFFGVLAVFSSVIYIGGLYPEKPANPRNYPFSGLAKDLGASSEEDTLLYAAKIDKSI E1UWC8 1.6.5.3 NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.009437788 1 LEVO MAGHGPHLLREDASFQRYGQLRDNLATYWKFNRKAARNVFIFLVAVPAGLGYLAYNYEGKTPFVGKRRTEPIFEQDYVPR K E1UWD7 1.6.5.3 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Komagataella pastoris 0.012845718 1 LEVO MSSIARKAVVPFSEANKKYVSSLYRKSLRTAHDWINKTEFYRVKASEIRSRFDANKHINDPNELKVIFKETEALLEDYAH PDPIIPPCRPGGSKFERNIPPRVEARIPIDV E1UWD2 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Komagataella pastoris 0.010473039 1 LEVO MGVSELPELLSHEEMKQNKIPLAYRDRCARLLVPLNKCRKEGWYMPWNCVQERHDYEQCQYLDFKRRVKELEEIKKQRDA ADASADL E1UWD9 NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) Komagataella pastoris 0.010787037 1 LEVO MVDHVRSPNVSFDDIDYNNSQDLHNAQESLLREQWIRVSALKVCRKALESCYKTSGPNHYEDCREIAEKYLNMLPDHRIQ GFLGYQKNDPSK E1UWC9 1.6.5.3 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit Komagataella pastoris 0.016331366 1 LEVO (ACE)SSSIQRTLRNLWKNGFKKSFKQLQGYNDIKSGRLVGTDSFGNKFYEVDDPVEIHMRTRFVEYTGFWRQDMSEVEP GWHYWLAYGTDVPPNQLKPEEKSVRAYPVKKHVPNLTYTDGAYVPYNTARPKCATWDPKVTERP E1UWE0 IRON/SULFUR CLUSTER 0.00035163999999999996 6 SF4 DIUNDECYL PHOSPHATIDYL CHOLINE 0.000622834 21 PLC FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN POTASSIUM ION 3.9098e-05 1 K 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 19 3PE CARDIOLIPIN 0.0014640429999999997 4 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 singleParticle particle 0.7 7.5 10.0 MOPS 50.0 KCl potassium chloride
10 mM MOPS, 50 mM KCl, pH 7.5 at 4 degrees celsius.
 Quantifoil R0.6/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR 0.039
Glow discharge 90s 20mA + chloroform and ethanol clean. Glow discharge 2X 90s 20mA, flipping in between.
 ETHANE 100 277.15 FEI VITROBOT MARK III
2s blot time and -10 blot force.
LMNG-solubilised Pichia Pastoris CI reconstituted in to nanodiscs (8:1:1 ratio of DOPC:DOPE:CDL [0.5 mg total] and 20 nM final Q10)
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.6 1.8 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 TFS FALCON 4i (4k x 4k) 4096 4096 1 7574 5.85 47.79 1 1350752 PHASE FLIPPING ONLY Initial model generated from 3D initial model job in CryoSPARC v3.3.2 C1 3.34 FSC 0.143 CUT-OFF 25125 PROJECTION MATCHING MAXIMUM LIKELIHOOD 4 40000.0
Not an even split in final numbers for the classes: class 1 53,716; class 2 61,256; class 3 25,125; class 4 18,608. Final classification used focused maps to target the compositionally heterogenous regions.
 emd_52876.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 501.66 501.66 501.66 90.0 90.0 90.0 X Y Z -0.026769355 0.07586619 -0.00010022779 0.0022485908 0.929 0.929 0.929 0.01 AUTHOR Final consensus map used for model building and model refinement. Globally sharpened with RELION postprocess. 9ihr PDB experimental model
taken from the state 1 model
The initial model was built into a map using ModelAngelo in RELION v5.0 for state 1. Appropriate subunits were deleted for this state before being manually inspected in Coot and final refinements with ligand restraints imposed performed in PHENIX v.1.21_5207
REAL emd_52876_msk_1.map emd_52876_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 501.66 501.66 501.66 90.0 90.0 90.0 X Y Z -0.04558611 0.06913028 -0.00010013624 0.005167414 0.929 0.929 0.929 AUTHOR Half map 1 emd_52876_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 540 540 540 0 0 0 540 540 540 501.66 501.66 501.66 90.0 90.0 90.0 X Y Z -0.046591908 0.06685915 -0.000100172256 0.0052298843 0.929 0.929 0.929 AUTHOR Half map 2