2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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 2025-02-21 2025-10-15 2025-10-15 2026-09-02 Medical Research Council (MRC, United Kingdom) MC_UU_00015/2 United Kingdom Closed state with NUQM and without flavoprotein (classification state 2) 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 9ihq FULLOVERLAP EMDB EMD-52877 associated EM volume
State 2 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 Komagataella pastoris 0.850 Altered inheritance of mitochondria protein 41, mitochondrial Komagataella pastoris 0.022019129 1 LEVO MFTLAARRLAIRLPRVRFGSSSAYDEALATIRNDLKLNFRFKADVLEKNVIRSILAETKNLEIDNKDKDLDEFKLYDLLS KMIKQRQDSAAIYLKEGSPDRFRQTGWNELREVDYITKYLEALPVASAEEIEAKVEPIVQSVLEEEGELKSPKEIFSRIP WKVVNQDWQASEGAVKNTVLRLYNLYKTDA C4QXX8 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 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 DIUNDECYL PHOSPHATIDYL CHOLINE 0.000622834 21 PLC IRON/SULFUR CLUSTER 0.00035163999999999996 5 SF4 FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 1 FES POTASSIUM ION 3.9098e-05 1 K 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 21 3PE CARDIOLIPIN 0.0014640429999999997 5 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 R1.2/1.3 COPPER CARBON HOLEY GLOW DISCHARGE AIR 0.039
glow discharged for 2X 90s, flipping the grid 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 2.9 FSC 0.143 CUT-OFF 61256 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_52877.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 -0.036482405 0.078555554 -0.000092214854 0.0032555202 0.929 0.929 0.929 0.0127 AUTHOR Consensus refinement map postprocessed with RELION and used for model building and model refinement 9IHR PDB experimental model
State 1 from same data
The initial model was made for state 1 and then subunits removed to match this state. This was manually inspected in Coot and final refinements with ligand restraints imposed performed in PHENIX v.1.21_5207
REAL emd_52877_msk_1.map emd_52877_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 -0.032965407 0.067039415 -0.00009142658 0.0040636337 0.929 0.929 0.929 AUTHOR Half map 1 emd_52877_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 -0.035034772 0.065295294 -0.00009291413 0.004053586 0.929 0.929 0.929 AUTHOR Half map 2