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- EMDB-11243: Membrane domain of closed complex I during turnover -

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Basic information

Entry
Database: EMDB / ID: EMD-11243
TitleMembrane domain of closed complex I during turnover
Map dataOversampled, local resolution-filtered map
Sample
  • Complex: Membrane domain of closed complex I during turnover
    • Protein or peptide: x 29 types
  • Ligand: x 7 types
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / reactive oxygen species metabolic process / mitochondrial intermembrane space ...NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / reactive oxygen species metabolic process / mitochondrial intermembrane space / fatty acid biosynthetic process / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrial matrix
Similarity search - Function
NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) ...NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Complex 1 LYR protein domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / Complex 1 protein (LYR family) / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 ...NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKampjut D / Sazanov LA
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Commission665385European Union
European Commission653706European Union
CitationJournal: Science / Year: 2020
Title: The coupling mechanism of mammalian respiratory complex I.
Authors: Domen Kampjut / Leonid A Sazanov /
Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
History
DepositionJun 30, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zkb
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zkb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11243.png

Downloads & links

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Map

FileDownload / File: emd_11243.map.gz / Format: CCP4 / Size: 163.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOversampled, local resolution-filtered map
Voxel sizeX=Y=Z: 0.5 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.29383627 - 0.5929758
Average (Standard dev.)0.012114053 (±0.05152325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions289313475
Spacing313289475
CellA: 156.5 Å / B: 144.5 Å / C: 237.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.50.50.5
M x/y/z313289475
origin x/y/z0.0000.0000.000
length x/y/z156.500144.500237.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS313289475
D min/max/mean-0.2940.5930.012

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Supplemental data

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Sample components

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Entire : Membrane domain of closed complex I during turnover

EntireName: Membrane domain of closed complex I during turnover
Components
  • Complex: Membrane domain of closed complex I during turnover
    • Protein or peptide: Mitochondrial complex I, 49 kDa subunit
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 5
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 2
    • Protein or peptide: Mitochondrial complex I, B14.7 subunit
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit B5
    • Protein or peptide: Acyl carrier protein
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
    • Protein or peptide: Mitochondrial complex I, PDSW subunit
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit S5
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit A3
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit B3
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 subunit C2
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit B4
    • Protein or peptide: Mitochondrial complex I, B16.6 subunit
    • Protein or peptide: Mitochondrial complex I, B17 subunit
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit B7
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit B9
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit B2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
    • Protein or peptide: Mitochondrial complex I, ESSS subunit
    • Protein or peptide: Mitochondrial complex I, KFYI subunit
    • Protein or peptide: Mitochondrial complex I, MNLL subunit
    • Protein or peptide: Mitochondrial complex I, MWFE subunit
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4L
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CARDIOLIPIN
  • Ligand: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: MYRISTIC ACID
  • Ligand: water

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Supramolecule #1: Membrane domain of closed complex I during turnover

SupramoleculeName: Membrane domain of closed complex I during turnover / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#29
Source (natural)Organism: Ovis aries (sheep)
Molecular weightExperimental: 1 MDa

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Macromolecule #1: Mitochondrial complex I, 49 kDa subunit

MacromoleculeName: Mitochondrial complex I, 49 kDa subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 52.017766 KDa
SequenceString: MAALRALRRL RGAAAQVLRP GAGARLPIQP SRGARQWQPD VEWAEQYGGA VMYPTKETAH WKPPPWNDVD PPKDTLVSNL TLNFGPGVL RLVMELSGEM VRKCDPHIGL LH(2MR)GTEKLIE YKTYLQALPY FDRLDYVSMM CNEQAYSLAV EKLLNIQ PP PRAQWIRVLF ...String:
MAALRALRRL RGAAAQVLRP GAGARLPIQP SRGARQWQPD VEWAEQYGGA VMYPTKETAH WKPPPWNDVD PPKDTLVSNL TLNFGPGVL RLVMELSGEM VRKCDPHIGL LH(2MR)GTEKLIE YKTYLQALPY FDRLDYVSMM CNEQAYSLAV EKLLNIQ PP PRAQWIRVLF GEITRLLNHI MAVTTHALDI GAMTPFFWMF EEREKMFEFY ERVSGARMHA AYVRPGGVHQ DLPLGLMD D IYEFSKNFSL RIDELEEMLT NNRIWRNRTV DIGVVTAEDA LNYGFSGVML RGSGIQWDLR KTQPYDVYDQ VEFDVPIGS RGDCYDRYLC RVEEMRQSIR IISQCLNKMP PGEIKVDDAK VSPPKRAEMK TSMESLIHHF KLYTEGYQVP PGATYTAIEA PKGEFGVYL VSDGSSRPYR CKIKAPGFAH LAGLDKMSKG HMLADVVAII GTQDIVFGEV DR

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Macromolecule #2: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 68.438906 KDa
SequenceString: (FME)NLFSSLTLV TLILLTMPIA AINFNTHKFT NYPLYVKTTI SCAFITSMIP TMMFIHTGQE MIISNWHWLT IQTLKL SLS FKMDFFSMMF VPVALFVTWS IMEFSMWYMH SDPNINQFFK YLLLFLITML ILVTANNLFQ LFIGWEGVGI MSFLLIG WW YGRTDANTAA ...String:
(FME)NLFSSLTLV TLILLTMPIA AINFNTHKFT NYPLYVKTTI SCAFITSMIP TMMFIHTGQE MIISNWHWLT IQTLKL SLS FKMDFFSMMF VPVALFVTWS IMEFSMWYMH SDPNINQFFK YLLLFLITML ILVTANNLFQ LFIGWEGVGI MSFLLIG WW YGRTDANTAA LQAILYNRIG DIGFILAMAW FLINLNTWDL QQIFMLNPND SNLPLMGLIL AATGKSAQFG LHPWLPSA M EGPTPVSALL HSSTMVVAGI FLLIRFYPLT ENNKFGQSIM LCLGAMTTLF TAMCALTQND IKKIIAFSTS SQLGLMMVT IGINQPHLAF LHICTHAFFK AMLFMCSGSI IHSLNDEQDI RKMGGLFKAM PFTTTALIIG SLALTGMPFL TGFYSKDLII ESANTSYTN AWALLMTLVA TSFTAIYSTR IIFFALLGQP RFPTLININE NNPFLINSIK RLLIGSLFAG FIISNNIPPM T IPQMTMPH YLKMTALTVT ILGFILALEI SNTTHYLKFN YPSNTFKFSN LLGYYPTIMH RLTPYMNLTM SQKSASSLLD LI WLETILP KTISLAQMKM STTITSQKGL IKLYFLSFLI TILISTTLLN FHE

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Macromolecule #3: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 52.086742 KDa
SequenceString: (FME)LKYIIPTMM LMPLTWLSKN SMIWINTTLH SLLISLTSLL LLNQFGDNSL NFSLTFFSDS LSTPLLILTM WLLPLM LMA SQHHLSKENL ARKKLFISML ILLQLFLIMT FTATELIFFY IMFEATLVPT LIIITRWGNQ TERLNAGLYF LFYTLAG SL PLLVALIYIQ ...String:
(FME)LKYIIPTMM LMPLTWLSKN SMIWINTTLH SLLISLTSLL LLNQFGDNSL NFSLTFFSDS LSTPLLILTM WLLPLM LMA SQHHLSKENL ARKKLFISML ILLQLFLIMT FTATELIFFY IMFEATLVPT LIIITRWGNQ TERLNAGLYF LFYTLAG SL PLLVALIYIQ NTMGSLNFLI LQYWVQPMPN SWSNTFMWLA CMMAFMVKMP LYGLHLWLPK AHVEAPIAGS MVLAAILL K LGGYGMMRIT LLLNPITDFM AYPFIMLSLW GMIMTSSICL RQTDLKSLIA YSSVSHMALV IVAILIQTPW SYMGATALM IAHGLTSSML FCLANSNYER VHSRTMILAR GLQTLLPLMA AWWLLASLTN LALPPSINLI GELFVVMSTF SWSNITIILM GLNMVITAL YSLYMLITTQ RGKHTHHINN ILPSFTRENA LMSLHMLPLL LLSLNPKIIL GPLY

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Macromolecule #4: NADH-ubiquinone oxidoreductase chain 2

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 39.149805 KDa
SequenceString: MNPIILIIIL MTVMLGTIIV MISTHWLLIW IGFEMNMLAI IPIMMKKHNP RATEASTKYF LTQSTASMLL MMAIIINLMF SGQWTVMKL FNPMASMLMT MALAMKLGMA PFHFWVPEVT QGIPLSSGLI LLTWQKLAPM SVLYQILPSI NLDLILTLSI L SITIGGWG ...String:
MNPIILIIIL MTVMLGTIIV MISTHWLLIW IGFEMNMLAI IPIMMKKHNP RATEASTKYF LTQSTASMLL MMAIIINLMF SGQWTVMKL FNPMASMLMT MALAMKLGMA PFHFWVPEVT QGIPLSSGLI LLTWQKLAPM SVLYQILPSI NLDLILTLSI L SITIGGWG GLNQTQLRKI MAYSSIAHMG WMTAVLLYNP TMTLLNLIIY IIMTSTMFTL FMANSTTTTL SLSHTWNKAP IM TILVLIT LLSMGGLPPL SGFMPKWMII QEMTKNDSII LPTLMAITAL LNLYFYMRLT YSTALTMFPS TNNMKMKWQF PTT KRMTLL PTMTVLSTML LPLTPILSIL E

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Macromolecule #5: Mitochondrial complex I, B14.7 subunit

MacromoleculeName: Mitochondrial complex I, B14.7 subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 14.784009 KDa
SequenceString:
M(AYA)KTLLHQYW DIPEGTECHR KTYAATSIGG ASGLVVSAYS VALKTPTSFL EGVARTGRYT FTAAAIGAIF GLTSCI SAQ VREKPDDPLN YLIGGCAGGL TLGARTRSYG IGAAACAYMG LTAALVKMGQ LEGWKVFAEP KV

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Macromolecule #6: NADH:ubiquinone oxidoreductase subunit B5

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit B5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 21.614201 KDa
SequenceString:
MAAMSLLHRA SVSAVVALSG RRLGTRLGFG GFLTRDFPKT VAPVRHSGDH GKRLFIIKPS GFYDKRFLKL LRFYILLTGI PVVIGITLI NVFIGEAELA EIPEGYVPEH WEYFKHPISR WIARTFFDAP EKNYERTMAI LQIESEKAEL RLKELEVRRL M RAKGDGPW FQYPTIDKAL IDHSPKATPD N

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Macromolecule #7: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 17.608199 KDa
SequenceString:
VEVKDFYTTN YQTAVSFSPL GPMPSMALMA VSLSGANVPK SGGRPEESRV PVLTQRKVPG RVTPLCRQYS DAPPLTLEGI KDRVLYVLK LYDKIDPEKL SVNSHFMKDL GLDSLDQVEI IMAMEDEFGF EIPDIDAEKL MCPQEIVDYI ADKKDVYE

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Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 20.139209 KDa
SequenceString:
MPGIVELPSL EDLKVQEVKV SSSVLKAAAH HYGAQCDKPN KEFMLCRWEE KDPRRCLEEG KLVNQCALEF FRQIKRHCAE PFTEYWTCI DYSGLQLFRR CRKEQAQFDK CVLDKLGWVR PDLGELSKVT KVKTDRPLPE NPYHSRARPE PNPEVEGDLK P ARHGSRLF FWTM

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Macromolecule #9: Mitochondrial complex I, PDSW subunit

MacromoleculeName: Mitochondrial complex I, PDSW subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 20.880752 KDa
SequenceString:
PDSWDKDVYP EPPRRTPAPS PQTSLPNPIT YLTKAFDLLV DRPVTLVREF IERQHAKNKY YYYHREFRRV PDITECHEKD VLCMFEAEM QWKRDYKVDQ EIVNIIQERL KACQQREGES HRQNCAKELQ QFTQVVKAYQ DRYHDLGAHY SARKCLAKQK Q RMLAERKA TKEAAAA

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Macromolecule #10: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 40.557148 KDa
SequenceString: MALRFLRLVP ASAASRGLAA VPPRVGGIHT SVQRKLQYGP LAYILGEKTT KKMTENSKLI TVDGNICSGK (SEP)KLAKE VAE KLGLKHFPEA GIHYADSTTG DGKPLPVRFS GNCSLEKFYD DPKSNDGNSY RLQAWLYASR LLQYADALEH LLSTGQG VV LERSIYSDFV ...String:
MALRFLRLVP ASAASRGLAA VPPRVGGIHT SVQRKLQYGP LAYILGEKTT KKMTENSKLI TVDGNICSGK (SEP)KLAKE VAE KLGLKHFPEA GIHYADSTTG DGKPLPVRFS GNCSLEKFYD DPKSNDGNSY RLQAWLYASR LLQYADALEH LLSTGQG VV LERSIYSDFV FLEAMYRQGF IRKQCVDHYN QVKKVTVCEY LPPHVVIYVD VPVSEVQSRI QKKGNPHEMK ITSAYLQD I ENVYKGTFLP EMSEKCEVLQ YSAWEAEDAE KVVEDIQYLK YDKGPWLDQD DRKLHNLRML VQDKLEVLNY TSIPVFLPE VTIGAHQSDR VFQEFTELPG RKYRAGYNED VGDKWIWLK

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Macromolecule #11: NADH:ubiquinone oxidoreductase subunit S5

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit S5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 12.605594 KDa
SequenceString:
MPFFDVQKKL GVDLDHWMTI QSAEQPHRIP ARCHAFEKEW IECAHGIGSI RAEKECKIEF EDFRECLLRQ KTMKRLNAIK RQRDKLIKE GKYTPPPHHS GQEDLRP

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Macromolecule #12: NADH:ubiquinone oxidoreductase subunit A3

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit A3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 9.325851 KDa
SequenceString:
MAPRVAAFLK NVWAKEPVLV ASFAIAGLAV ILPTLSPYTK YSLMINRATP YNYPVPLRDD GNMPDVPSHP QDPQGPSLEW LKRL

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Macromolecule #13: NADH:ubiquinone oxidoreductase subunit B3

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit B3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 11.146679 KDa
SequenceString:
MAHGHGHEHG PSKMELPDYK QWKIEGTPLE TVQEKLAARG LRDPWGRNEA WRYMGGFANN VSFVGALLKG FKWGFAAFVV AVGAEYYLE SQKKDKKHH

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Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 subunit C2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 14.431655 KDa
SequenceString:
VTMMTGRQAR APLQFLPDEA RSLPPPKLTD PRLAYIGFLG YCSGLIDNAI RRRPVLSAGL HRQFLYITSF VFVGYYLLKR QDYMYAVRD HDMFSYIKSH PEDFPEKDKK TYREVFEEFH PVR

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Macromolecule #15: NADH:ubiquinone oxidoreductase subunit B4

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit B4 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 15.236375 KDa
SequenceString:
KMSFPKYEPS RLASLPTTLD PAEYDISSET RKAQAERLAI RSRLKREYQL QYNDPSRRGV VEDPALIRWT CARSANVYPN FRPNTKTSL LGALFGIGPL IFWYYVFKTD RDRKEKLIQE GKLDRTFNIS Y

+
Macromolecule #16: Mitochondrial complex I, B16.6 subunit

MacromoleculeName: Mitochondrial complex I, B16.6 subunit / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 16.766461 KDa
SequenceString:
MAASKVKQDM PPVGGYGPID YKRNLPRRGL SGYSMFAVGI GALLFGYWSM MRWNRERRRL QIEDFEARIA LMPLLQAEKD RRVLQMLRE NLEEEATIMK DVPGWKVGES VFHTTRWVTP MMGELYGLRT GEEILSSTYG FIWYT

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Macromolecule #17: Mitochondrial complex I, B17 subunit

MacromoleculeName: Mitochondrial complex I, B17 subunit / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 15.565126 KDa
SequenceString:
MSGYTPDEKL RLQQLRELRR RWLKDQELSP REPVLPPRRV SPVERFWNKF LQDGALWKNV IYKTYRHSIF AFTHVLIPVW IIHYYLKYH VTTKPYTIVE KKPRIFPGDT ILETGEVIPP MKEFPDQHH

+
Macromolecule #18: NADH:ubiquinone oxidoreductase subunit B7

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit B7 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 16.413807 KDa
SequenceString:
MGAHLARRYL GDASVEPEPL RMPTFPPDYG FPERKEREMV ATQQEMNDAQ LVLQQRDYCA HYLIRFLKCK RDSFPNFLAC KHEQHDWDY CEHLDYVKRM KEFERERRLL QRKKRREQRE ADMAKGLGPG EVAPEVAL

+
Macromolecule #19: NADH:ubiquinone oxidoreductase subunit B9

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit B9 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 21.77991 KDa
SequenceString:
MAFLPSAAYL THQQKVLQLY KRALRHLESR CVHRDKYRYF ACLLRARFDE HKNEKDMVKA TQLLREAEKE FWHGQHPQPY IFPESPGGT SYERYECYKV PEWCLDDWHP SEKAMYPDYF AKREQWKKLR RESWEREVKQ LQEETPVGGP RTEALPPARK Q GDLPPLWW HIVTRPRERP M

+
Macromolecule #20: NADH:ubiquinone oxidoreductase subunit B2

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit B2 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 12.22677 KDa
SequenceString:
MAGMSALKRL APFAHVGGHL FRGRCARAVG AGGVRRAGGG AHIEPRYRQF PQLTRSQVIQ AEFFSATMWF WILWRFWHDS DAVLGHFPY PDPSQWTDEE LGIPPDDED

+
Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 21.752602 KDa
SequenceString:
MAAARAGVLG IRWLQKAARN VVPLGARTAS HITKDMLPGP YPKTPEERAA AAKKYNMRVE DYEPYPDDGM GYGDYPKLPD RSQQERDPW YDWDHPDLRL NWGEPMHWDL DMYIRNRVDT SPTPVNWNLM CKHLFGFVAF MLFMFWVGET YPTYQPVGPK Q YPYNNLYL ERGGDPNKEP EPVVHYEI

+
Macromolecule #22: Mitochondrial complex I, ESSS subunit

MacromoleculeName: Mitochondrial complex I, ESSS subunit / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 17.41066 KDa
SequenceString:
MAAGMLGLCG RRLLAVAATR GLPAASVRWE SSSSRAVIAP STLAGKRPSE PTLRWQEDPE PEDENLYEKN PDSHGYDKDP AVDVWNMRV VFFFGFSIVL VLGSTFVAYL PDYRMQEWAR REAERLVKYR EAHGLPLMES NCFDPSKIQL PEDED

+
Macromolecule #23: Mitochondrial complex I, KFYI subunit

MacromoleculeName: Mitochondrial complex I, KFYI subunit / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 8.802174 KDa
SequenceString:
MAPSAFLRPF WKLLAPARFP SVSSSRSKFY IQEPPHGSPN WLKVGLTLGT SAFLWIYLIK QHNEDVLEYK RRNGLE

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Macromolecule #24: Mitochondrial complex I, MNLL subunit

MacromoleculeName: Mitochondrial complex I, MNLL subunit / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 7.075305 KDa
SequenceString:
MMNLLQVVRD HWIHVLVPVG FVFGYYLDRK NDEKLAAFRN KSLLYKRELK PQEEVTWK

+
Macromolecule #25: Mitochondrial complex I, MWFE subunit

MacromoleculeName: Mitochondrial complex I, MWFE subunit / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 8.211519 KDa
SequenceString:
MWFEVLPGIA VMGVCLFIPG MATARIHRFS NGGREKRVAH YSYQWYLMER DRRVSGVNRY YVSKGLENID

+
Macromolecule #26: NADH-ubiquinone oxidoreductase chain 3

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 3 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 13.10652 KDa
SequenceString:
MNLMITLLTN FTLATLLVTI AFWLPQLNVY SEKTSPYECG FDPMGSARLP FSMKFFLVAI TFLLFDLEIA LLLPLPWASQ TTNLNTMLT MALLLIFLLA VSLAYEWTQK GLEWTE

+
Macromolecule #27: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 35.884902 KDa
SequenceString: MFMINVLTLI IPILLAVAFL TLVERKVLGY MQFRKGPNVV GPYGLLQPIA DAIKLFIKEP LRPATSSISM FILAPILALT LALTMWIPL PMPYPLINMN LGVLFMLAMS SLAVYSILWS GWASNSKYAL IGALRAVAQT ISYEVTLAII LLSVLLMNGS F TLSTLIIT ...String:
MFMINVLTLI IPILLAVAFL TLVERKVLGY MQFRKGPNVV GPYGLLQPIA DAIKLFIKEP LRPATSSISM FILAPILALT LALTMWIPL PMPYPLINMN LGVLFMLAMS SLAVYSILWS GWASNSKYAL IGALRAVAQT ISYEVTLAII LLSVLLMNGS F TLSTLIIT QEQVWLIFPA WPLAMMWFIS TLAETNRAPF DLTEGESELV SGFNVEYAAG PFALFFMAEY ANIIMMNIFT TT LFLGAFH NPYMPELYTI NFTIKSLLLS ITFLWIRASY PRFRYDQLMH LLWKNFLPLT LALCMWHVSL PILLSSIPPQ T

+
Macromolecule #28: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 19.126619 KDa
SequenceString:
MMTYIVFILS IIFVMGFVGF SSKPSPIYGG LGLIVSGGVG CGIVLNFGGS FLGLMVFLIY LGGMMVVFGY TTAMATEQYP EVWVSNKVV LGTFITGLLM EFLMVYYVLK DKEVEIVFKF NGMGDWVIYD TGDSGFFSEE AMGIAALYSY GTWLVIVTGW S LLIGVVVI MEITRGN

+
Macromolecule #29: NADH-ubiquinone oxidoreductase chain 4L

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4L / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Sheep (sheep)
Molecular weightTheoretical: 10.868237 KDa
SequenceString:
(FME)SLVYMNIMM AFTVSLTGLL MYRSHLMSSL LCLEGMMLSL FILATLMILN SHFTLASMMP IILLVFAACE AALGLS LLV MVSNTYGTDY VQNLNLLQC

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Macromolecule #30: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 30 / Number of copies: 11 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da

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Macromolecule #31: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 31 / Number of copies: 4 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #32: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 32 / Number of copies: 7 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #33: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
type: ligand / ID: 33 / Number of copies: 1 / Formula: ZMP
Molecular weightTheoretical: 568.704 Da
Chemical component information

ChemComp-ZMP:
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate

+
Macromolecule #34: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 34 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

+
Macromolecule #35: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 35 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

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Macromolecule #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 446 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.15)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5lnk

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 29057
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5lnk

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 50 / Target criteria: Correlation coefficient
Output model

PDB-6zkb:
Membrane domain of closed complex I during turnover

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