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- PDB-7vbp: Membrane arm of deactive state CI from DQ-NADH dataset -

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Entry
Database: PDB / ID: 7vbp
TitleMembrane arm of deactive state CI from DQ-NADH dataset
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
KeywordsELECTRON TRANSPORT / Respiratory / Complex
Function / homology
Function and homology information


Mitochondrial protein import / Respiratory electron transport / Complex I biogenesis / Neutrophil degranulation / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone ...Mitochondrial protein import / Respiratory electron transport / Complex I biogenesis / Neutrophil degranulation / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H / 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 / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / reactive oxygen species metabolic process / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / nuclear speck / endoplasmic reticulum / mitochondrion / nucleoplasm / cytoplasm
Similarity search - Function
NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 ...NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / 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 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / 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 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-quinone oxidoreductase, chain 5-like / CHCH / CHCH domain / 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-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Complex 1 protein (LYR family) / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / [NiFe]-hydrogenase, large subunit / 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
Chem-8Q1 / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 ...Chem-8Q1 / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGu, J.K. / Yang, M.J.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504600 and 2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31625008, 32030056, 21532004, 31570733, 31800620 China
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: The coupling mechanism of mammalian mitochondrial complex I.
Authors: Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang /
Abstract: Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in ...Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
U: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
X: Acyl carrier protein, mitochondrial
Y: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
a: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
b: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
c: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
e: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
f: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
g: NADH dehydrogenase [ubiquinone] 1 subunit C2
h: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
i: NADH-ubiquinone oxidoreductase chain 2
j: NADH-ubiquinone oxidoreductase chain 3
k: NADH-ubiquinone oxidoreductase chain 4L
l: NADH-ubiquinone oxidoreductase chain 5
m: NADH-ubiquinone oxidoreductase chain 6
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
r: NADH-ubiquinone oxidoreductase chain 4
s: NADH-ubiquinone oxidoreductase chain 1
u: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
v: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
w: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,76550
Polymers547,10629
Non-polymers19,65921
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 2 types, 2 molecules Qh

#1: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH-ubiquinone oxidoreductase 49 kDa subunit / Complex I-49kD


Mass: 4696.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JYS1
#16: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH-ubiquinone oxidoreductase 15 kDa subunit / Complex I-15 kDa


Mass: 12375.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules SUVWuw

#2: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Complex I-MWFE


Mass: 8088.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43
#3: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B9 subunit / Complex I-B9


Mass: 9094.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VQ42
#4: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase subunit B14.7 / Complex I-B14.7


Mass: 14555.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#5: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase B16.6 subunit / Complex I-B16.6


Mass: 13522.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S6Q1
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase 19 kDa subunit / Complex I-19kD


Mass: 19932.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1
#29: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 36792.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9

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Protein , 1 types, 1 molecules X

#6: Protein Acyl carrier protein, mitochondrial


Mass: 10133.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G781

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopv

#7: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH-ubiquinone oxidoreductase AGGG subunit / Complex I-AGGG


Mass: 8430.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V766
#8: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit / Complex I-B12


Mass: 9504.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AS93
#9: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH-ubiquinone oxidoreductase SGDH subunit / Complex I-SGDH


Mass: 16477.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#10: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH-ubiquinone oxidoreductase B17 subunit / Complex I-B17


Mass: 15333.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN80
#11: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18608.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#12: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase PDSW subunit / Complex I-PDSW


Mass: 20813.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYV0
#13: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 12635.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MNLL subunit / Complex I-MNLL


Mass: 6781.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SD73
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH-ubiquinone oxidoreductase B15 subunit / Complex I-B15


Mass: 14986.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase B22 subunit / Complex I-B22


Mass: 21733.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T0A8
#28: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH-ubiquinone oxidoreductase B18 subunit / Complex I-B18


Mass: 15954.306 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg

#14: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase KFYI subunit / Complex I-KFYI


Mass: 4945.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQS6
#15: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14196.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmrs

#17: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating)
#18: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12798.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating)
#19: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating)
#20: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 68267.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q71K68, NADH:ubiquinone reductase (H+-translocating)
#21: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating)
#25: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 51853.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q7IIB7, NADH:ubiquinone reductase (H+-translocating)
#26: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 7 types, 370 molecules

#30: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#31: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#32: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C42H89NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#34: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#36: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 387112 / Symmetry type: POINT

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