5O31

Mitochondrial complex I in the deactive state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.13 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

Structure of the Deactive State of Mammalian Respiratory Complex I.

Blaza, J.N.Vinothkumar, K.R.Hirst, J.

(2018) Structure 26: 312-319.e3

  • DOI: 10.1016/j.str.2017.12.014
  • Primary Citation of Related Structures:  
    5O31

  • PubMed Abstract: 
  • Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis ...

    Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.


    Organizational Affiliation

    MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK. Electronic address: jh@mrc-mbu.cam.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A115Bos taurusMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P03898 (Bos taurus)
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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
Find proteins for P23709 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialD430Bos 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 
UniProt
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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 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialF464Bos taurusMutation(s): 0 
Gene Names: NDUFV1UQOR1
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 chain 1G [auth H]318Bos taurusMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialH [auth I]176Bos 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: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6I [auth J]175Bos taurusMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LJ [auth K]98Bos taurusMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
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 5K [auth L]606Bos taurusMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
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 4L [auth M]459Bos taurusMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
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 2M [auth N]347Bos taurusMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialN [auth O]320Bos taurusMutation(s): 0 
Gene Names: NDUFA10
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9O [auth P]297Bos taurusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2P [auth S]98Bos taurusMutation(s): 0 
Gene Names: NDUFA2
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialQ [auth T], R [auth U]88Bos taurusMutation(s): 0 
Gene Names: NDUFAB1
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5S [auth V]115Bos taurusMutation(s): 0 
Gene Names: NDUFA5
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6T [auth W]128Bos taurusMutation(s): 0 
Gene Names: NDUFA6
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11U [auth Y]141Bos taurusMutation(s): 0 
Gene Names: NDUFA11
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1V [auth a]70Bos taurusMutation(s): 0 
Gene Names: NDUFA1
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3W [auth b]80Bos taurusMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialX [auth c]49Bos taurusMutation(s): 0 
Gene Names: NDUFC1
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5Y [auth e]105Bos taurusMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1Z [auth f]57Bos taurusMutation(s): 0 
Gene Names: NDUFB1
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialAA [auth g]125Bos taurusMutation(s): 0 
Gene Names: NDUFB11
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6BA [auth i]111Bos taurusMutation(s): 0 
Gene Names: NDUFB6
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2CA [auth j]52Bos taurusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3DA [auth k]74Bos taurusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8EA [auth l]120Bos taurusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7FA [auth o]136Bos taurusMutation(s): 0 
Gene Names: NDUFB7
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10GA [auth p]169Bos taurusMutation(s): 0 
Gene Names: NDUFB10
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12HA [auth q]145Bos taurusMutation(s): 0 
Gene Names: NDUFA12
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialIA [auth G]704Bos 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 
UniProt
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialJA [auth s]75Bos taurusMutation(s): 0 
Gene Names: NDUFV3
Membrane Entity: Yes 
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialKA [auth Q]133Bos taurusMutation(s): 0 
Gene Names: NDUFS4
Membrane Entity: Yes 
UniProt
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialLA [auth R]96Bos taurusMutation(s): 0 
Gene Names: NDUFS6
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7MA [auth r]112Bos taurusMutation(s): 0 
Gene Names: NDUFA7CI-B14-5A
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialNA [auth h]143Bos taurusMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2OA [auth d]116Bos taurusMutation(s): 0 
Gene Names: NDUFC2
Membrane Entity: Yes 
UniProt
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8PA [auth X]171Bos taurusMutation(s): 0 
Gene Names: NDUFA8
Membrane Entity: Yes 
UniProt
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4QA [auth m]128Bos taurusMutation(s): 0 
Gene Names: NDUFB4
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9RA [auth n]178Bos taurusMutation(s): 0 
Gene Names: NDUFB9UQOR22
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13SA [auth Z]144Bos taurusMutation(s): 0 
Gene Names: NDUFA13
Membrane Entity: Yes 
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

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ZA [auth P]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
FMN
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

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AB [auth G], BB [auth G], TA [auth B], WA [auth F], XA [auth I], YA [auth I]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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CB [auth G], UA [auth E]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: 4.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105663141
Medical Research Council (United Kingdom)United KingdomU105184322

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Data processing
  • Version 1.2: 2018-03-21
    Changes: Database references
  • Version 1.3: 2018-10-10
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.4: 2019-10-23
    Changes: Data collection, Other, Structure summary