7VYH

Matrix arm of deactive state CI from Rotenone dataset

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2021-11-14 Released: 2022-11-23 
  • Deposition Author(s): Gu, J.K., Yang, M.J.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The coupling mechanism of mammalian mitochondrial complex I.

Gu, J.K.Liu, T.Guo, R.Zhang, L.Yang, M.J.

(2022) Nat Struct Mol Biol 29: 172-182

  • DOI: 10.1038/s41594-022-00722-w
  • Primary Citation of Related Structures:  
    7V2C, 7V2D, 7V2E, 7V2F, 7V2H, 7V2K, 7V2R, 7V30, 7V31, 7V32, 7V33, 7V3M, 7VB7, 7VBL, 7VBN, 7VBP, 7VBZ, 7VC0, 7VWJ, 7VWL, 7VYF, 7VYG, 7VYH, 7VYI

  • PubMed 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 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 ...

    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.


    Organizational Affiliation

    SUSTech Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen, China. maojunyang@tsinghua.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA431Sus scrofaMutation(s): 0 
Gene Names: NDUFV1
EC: 7.1.1.2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialB176Sus scrofaMutation(s): 0 
Gene Names: NDUFS8
UniProt
Find proteins for A0A287BDC0 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialC156Sus scrofaMutation(s): 0 
Gene Names: NDUFS7
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth E]115Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2E [auth F]86Sus scrofaMutation(s): 0 
Gene Names: NDUFA2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinF [auth G]88Sus scrofaMutation(s): 0 
Gene Names: NDUFAB1
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5G [auth H]112Sus scrofaMutation(s): 0 
Gene Names: NDUFA5
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7H [auth I]112Sus scrofaMutation(s): 0 
Gene Names: NDUFA7
UniProt
Find proteins for A0A4X1VLA2 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrialI [auth J]341Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialJ [auth K]42Sus scrofaMutation(s): 0 
Gene Names: NDUFV3
UniProt
Find proteins for A0A4X1TFI3 (Sus scrofa)
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Entity ID: 11
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth L]125Sus scrofaMutation(s): 0 
UniProt
Find proteins for G8IFA6 (Sus scrofa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialL [auth M]690Sus scrofaMutation(s): 0 
Gene Names: NDUFS1
UniProt
Find proteins for F1SHD7 (Sus scrofa)
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Entity ID: 13
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12M [auth N]144Sus scrofaMutation(s): 0 
Gene Names: NDUFA12
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialN [auth O]217Sus scrofaMutation(s): 0 
Gene Names: NDUFV2
UniProt
Find proteins for A0A287BG40 (Sus scrofa)
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Entity ID: 15
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialO [auth P]208Sus scrofaMutation(s): 0 
Gene Names: NDUFS3
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialP [auth Q]385Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JYS1 (Sus scrofa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialQ [auth T]96Sus scrofaMutation(s): 0 
Gene Names: NDUFS6
UniProt
Find proteins for F1S031 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13R [auth W]29Sus scrofaMutation(s): 0 
Gene Names: NDUFA13
UniProt
Find proteins for F1S6Q1 (Sus scrofa)
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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FA [auth N]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PLX (Subject of Investigation/LOI)
Query on PLX

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Y [auth C](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
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
 Ligand Interaction
NDP (Subject of Investigation/LOI)
Query on NDP

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AA [auth J]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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X [auth C]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

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Z [auth G]S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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T [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4 (Subject of Investigation/LOI)
Query on SF4

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BA [auth M],
CA [auth M],
S [auth A],
U [auth B],
V [auth B],
BA [auth M],
CA [auth M],
S [auth A],
U [auth B],
V [auth B],
W [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES (Subject of Investigation/LOI)
Query on FES

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DA [auth M],
GA [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

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HA [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

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EA [auth M]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
P [auth Q]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0504600 and 2016YFA0501100
National Natural Science Foundation of China (NSFC)China31625008
National Natural Science Foundation of China (NSFC)China32030056, 21532004 and 31570733 and 31800620

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release