6G72

Mouse mitochondrial complex I in the deactive state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states.

Agip, A.A., Blaza, J.N., Bridges, H.R., Viscomi, C., Rawson, S., Muench, S.P., Hirst, J.

(2018) Nat Struct Mol Biol 25: 548-556

  • DOI: 10.1038/s41594-018-0073-1
  • Primary Citation of Related Structures:  
    6G2J, 6G72

  • PubMed Abstract: 

    • Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-com ...

    Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-complete models of all 45 subunits in the bovine, ovine and porcine complexes and have identified two states relevant to complex I in ischemia-reperfusion injury. Here, we describe the 3.3-Å structure of complex I from mouse heart mitochondria, a biomedically relevant model system, in the 'active' state. We reveal a nucleotide bound in subunit NDUFA10, a nucleoside kinase homolog, and define mechanistically critical elements in the mammalian enzyme. By comparisons with a 3.9-Å structure of the 'deactive' state and with known bacterial structures, we identify differences in helical geometry in the membrane domain that occur upon activation or that alter the positions of catalytically important charged residues. Our results demonstrate the capability of cryo-EM analyses to challenge and develop mechanistic models for mammalian complex I.

    Organizational Affiliation: 

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK. jh@mrc-mbu.cam.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A115Mus musculusMutation(s): 0 
Gene Names: Mtnd3, mt-Nd3, Nd3
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6J172Mus musculusMutation(s): 0 
Gene Names: Mtnd6, mt-Nd6, Nd6
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LK98Mus musculusMutation(s): 0 
Gene Names: Mtnd4l, mt-Nd4l, Nd4l
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5L607Mus musculusMutation(s): 0 
Gene Names: Mtnd5, mt-Nd5, Nd5
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4M459Mus musculusMutation(s): 0 
Gene Names: Mtnd4, mt-Nd4, Nd4
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 14
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NADH-ubiquinone oxidoreductase chain 2N345Mus musculusMutation(s): 0 
Gene Names: Mtnd2, mt-Nd2, Nd2
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 15
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialO355Mus musculusMutation(s): 0 
Gene Names: Ndufa10
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NIH Common Fund Data Resources
IMPC  MGI:1914523
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Entity ID: 16
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialP377Mus musculusMutation(s): 0 
Gene Names: Ndufa9
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IMPC  MGI:1913358
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Entity ID: 17
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialQ175Mus musculusMutation(s): 0 
Gene Names: Ndufs4
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Entity ID: 18
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR116Mus musculusMutation(s): 0 
Gene Names: Ndufs6, Ip13
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Entity ID: 19
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2S99Mus musculusMutation(s): 0 
Gene Names: Ndufa2
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Entity ID: 2
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialB224Mus musculusMutation(s): 0 
Gene Names: Ndufs7
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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IMPC  MGI:1922656
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Entity ID: 20
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Acyl carrier protein, mitochondrialT, U156Mus musculusMutation(s): 0 
Gene Names: Ndufab1
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Entity ID: 21
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5V116Mus musculusMutation(s): 0 
Gene Names: Ndufa5
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Entity ID: 22
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6W131Mus musculusMutation(s): 0 
Gene Names: Ndufa6
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IMPC  MGI:1914380
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Entity ID: 23
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8X172Mus musculusMutation(s): 0 
Gene Names: Ndufa8
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IMPC  MGI:1915625
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Entity ID: 24
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11Y143Mus musculusMutation(s): 0 
Gene Names: Ndufa11
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Entity ID: 25
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13Z144Mus musculusMutation(s): 0 
Gene Names: Ndufa13, Grim19
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Entity ID: 26
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1a70Mus musculusMutation(s): 0 
Gene Names: Ndufa1
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Entity ID: 27
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3b84Mus musculusMutation(s): 0 
Gene Names: Ndufa3
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Entity ID: 28
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NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialc76Mus musculusMutation(s): 0 
Gene Names: Ndufc1
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Entity ID: 29
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NADH dehydrogenase [ubiquinone] 1 subunit C2d120Mus musculusMutation(s): 0 
Gene Names: Ndufc2
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Entity ID: 3
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialC263Mus musculusMutation(s): 0 
Gene Names: Ndufs3
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q9DCT2 (Mus musculus)
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IMPC  MGI:1915599
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5e106Mus musculusMutation(s): 0 
Gene Names: Ndufs5
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Entity ID: 31
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1f57Mus musculusMutation(s): 0 
Gene Names: Ndufb1
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Entity ID: 32
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialg151Mus musculusMutation(s): 0 
Gene Names: Ndufb11, Np15
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Entity ID: 33
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialh189Mus musculusMutation(s): 0 
Gene Names: Ndufb5
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Entity ID: 34
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6i128Mus musculusMutation(s): 0 
Gene Names: Ndufb6, Gm137
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialj105Mus musculusMutation(s): 0 
Gene Names: Ndufb2
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Entity ID: 36
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3k104Mus musculusMutation(s): 0 
Gene Names: Ndufb3
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Entity ID: 37
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondriall186Mus musculusMutation(s): 0 
Gene Names: Ndufb8
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IMPC  MGI:1914514
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4m129Mus musculusMutation(s): 0 
Gene Names: Ndufb4
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Entity ID: 39
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9n179Mus musculusMutation(s): 0 
Gene Names: Ndufb9
Find proteins for Q9CQJ8 (Mus musculus)
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IMPC  MGI:1913468
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Entity ID: 4
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialD463Mus musculusMutation(s): 0 
Gene Names: Ndufs2
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q91WD5 (Mus musculus)
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IMPC  MGI:2385112
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Entity ID: 40
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7o137Mus musculusMutation(s): 0 
Gene Names: Ndufb7
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Entity ID: 41
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10p176Mus musculusMutation(s): 0 
Gene Names: Ndufb10
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Entity ID: 42
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12q145Mus musculusMutation(s): 0 
Gene Names: Ndufa12
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7r113Mus musculusMutation(s): 0 
Gene Names: Ndufa7
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Entity ID: 44
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NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrials104Mus musculusMutation(s): 0 
Gene Names: Ndufv3
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Entity ID: 5
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NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialE248Mus musculusMutation(s): 0 
Gene Names: Ndufv2
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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Entity ID: 6
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialF464Mus musculusMutation(s): 0 
Gene Names: Ndufv1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q91YT0 (Mus musculus)
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IMPC  MGI:107851
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Entity ID: 7
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NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialG727Mus musculusMutation(s): 0 
Gene Names: Ndufs1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q91VD9 (Mus musculus)
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IMPC  MGI:2443241
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1H318Mus musculusMutation(s): 0 
Gene Names: Mtnd1, mt-Nd1, Nd1
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for P03888 (Mus musculus)
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Entity ID: 9
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialI212Mus musculusMutation(s): 0 
Gene Names: Ndufs8
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for Q8K3J1 (Mus musculus)
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IMPC  MGI:2385079
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP
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P
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N		 Ligand Interaction
EHZ
Query on EHZ
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T, U
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N		 Ligand Interaction
FMN
Query on FMN
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F
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
ADP
Query on ADP
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O
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
SF4
Query on SF4
Download CCD File 
B, F, G, I
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
Download CCD File 
E, G
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME		AL-PEPTIDE LINKINGC6 H11 N O3 SMET
AYA
Query on AYA		bL-PEPTIDE LINKINGC5 H9 N O3ALA
SAC
Query on SAC		iL-PEPTIDE LINKINGC5 H9 N O4SER
2MR
Query on 2MR		DL-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105663141
Medical Research Council (United Kingdom)United KingdomMC_UU_00015/2
Medical Research Council (United Kingdom)United KingdomMC_UU_00015/5

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-03
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-12-11
    Changes: Other