5LDW

Structure of mammalian respiratory Complex I, class1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of mammalian respiratory complex I.

Zhu, J., Vinothkumar, K.R., Hirst, J.

(2016) Nature 536: 354-358

  • DOI: 10.1038/nature19095
  • Primary Citation of Related Structures:  
    5LC5, 5LDX, 5LDW

  • PubMed Abstract: 

    • Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref ...

    Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref. 1) contains 45 subunits, comprising 14 core subunits that house the catalytic machinery (and are conserved from bacteria to humans) and a mammalian-specific cohort of 31 supernumerary subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis.

    Organizational Affiliation: 

    MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A115Bos taurusMutation(s): 0 
Gene Names: MT-ND3, MTND3, NADH3, ND3
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialB179Bos taurusMutation(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)
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialC228Bos taurusMutation(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)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialD429Bos taurusMutation(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)
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialE217Bos taurusMutation(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)
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialF444Bos taurusMutation(s): 0 
Gene Names: NDUFV1, UQOR1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialG785Bos taurusMutation(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)
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1H318Bos taurusMutation(s): 0 
Gene Names: MT-ND1, MTND1, NADH1, ND1
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialI176Bos taurusMutation(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)
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6J175Bos taurusMutation(s): 0 
Gene Names: MT-ND6, MTND6, NADH6, ND6
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LK98Bos taurusMutation(s): 0 
Gene Names: MT-ND4L, MTND4L, NADH4L, ND4L
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5L606Bos taurusMutation(s): 0 
Gene Names: MT-ND5, MTND5, NADH5, ND5
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4M459Bos taurusMutation(s): 0 
Gene Names: MT-ND4, MTND4, NADH4, ND4
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2N347Bos taurusMutation(s): 0 
Gene Names: MT-ND2, MTND2, NADH2, ND2
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialO316Bos taurusMutation(s): 0 
Gene Names: NDUFA10
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9P300Bos taurusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4Q113Bos taurusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, NDUFS6,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR89Bos taurusMutation(s): 0 
Gene Names: NDUFS6
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2S99Bos taurusMutation(s): 0 
Gene Names: NDUFA2
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialT, U88Bos taurusMutation(s): 0 
Gene Names: NDUFAB1
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5V115Bos taurusMutation(s): 0 
Gene Names: NDUFA5
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6W128Bos taurusMutation(s): 0 
Gene Names: NDUFA6
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, NDUFA8X169Bos taurusMutation(s): 0 
Gene Names: NDUFA8
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11Y141Bos taurusMutation(s): 0 
Gene Names: NDUFA11
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13Z138Bos taurusMutation(s): 0 
Gene Names: NDUFA13
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]70Bos taurusMutation(s): 0 
Gene Names: NDUFA1
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3, NDUFA3BA [auth b]80Bos taurusMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth c]49Bos taurusMutation(s): 0 
Gene Names: NDUFC1
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2DA [auth d]114Bos taurusMutation(s): 0 
Gene Names: NDUFC2
Membrane Entity: Yes 
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth e]105Bos taurusMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1FA [auth f]57Bos taurusMutation(s): 0 
Gene Names: NDUFB1
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialGA [auth g]125Bos taurusMutation(s): 0 
Gene Names: NDUFB11
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, NDUFB5HA [auth h]134Bos taurusMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6, NDUFB6IA [auth i]106Bos taurusMutation(s): 0 
Gene Names: NDUFB6
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2JA [auth j]52Bos taurusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3KA [auth k]74Bos taurusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8LA [auth l]118Bos taurusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth m]118Bos taurusMutation(s): 0 
Gene Names: NDUFB4
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9, NDUFB9NA [auth n]166Bos taurusMutation(s): 0 
Gene Names: NDUFB9
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7OA [auth o]136Bos taurusMutation(s): 0 
Gene Names: NDUFB7
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10PA [auth p]169Bos taurusMutation(s): 0 
Gene Names: NDUFB10
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12QA [auth q]145Bos taurusMutation(s): 0 
Gene Names: NDUFA12
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7RA [auth r]87Bos taurusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3SA [auth s]35Bos taurusMutation(s): 0 
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP
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 CB [auth P]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN
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 VA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
 AB [auth I], BB [auth I], TA [auth B], WA [auth F], XA [auth G], YA [auth G]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
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 UA [auth E], ZA [auth G]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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 DB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 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 KingdomU105184322/U105663141

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2019-10-23
    Changes: Data collection, Other