5LNK

Entire ovine respiratory complex I


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 1.3 of the entry. See complete history


Literature

Atomic structure of the entire mammalian mitochondrial complex I.

Fiedorczuk, K.Letts, J.A.Degliesposti, G.Kaszuba, K.Skehel, M.Sazanov, L.A.

(2016) Nature 538: 406-410

  • DOI: 10.1038/nature19794
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly ...

    Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.


    Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 51 kDa subunit1445Ovis ariesMutation(s): 0 
Gene Names: NDUFV1
EC: 1.6.99.3 (UniProt), 7.1.1.2 (UniProt)
Find proteins for W5PUX0 (Ovis aries)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 24 kDa subunit2217Ovis ariesMutation(s): 0 
Find proteins for W5NRY1 (Ovis aries)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 75 kDa subunit3704Ovis ariesMutation(s): 0 
Gene Names: NDUFS1
Find proteins for W5QB34 (Ovis aries)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 49 kDa subunit4412Ovis ariesMutation(s): 0 
Gene Names: NDUFS2
Find proteins for W5PJ73 (Ovis aries)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 30 kDa subunit5228Ovis ariesMutation(s): 0 
Gene Names: NDUFS3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, PSST subunit6179Ovis ariesMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, TYKY subunit9176Ovis ariesMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND1 subunitH318Ovis ariesMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
Find proteins for O78747 (Ovis aries)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND2 subunitN347Ovis ariesMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND3 subunitA115Ovis ariesMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
Find proteins for O78753 (Ovis aries)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND4 subunitM459Ovis ariesMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
EC: 7.1.1.2
Find proteins for O78755 (Ovis aries)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND4L subunitK98Ovis ariesMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND5 subunitL599Ovis ariesMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
EC: 7.1.1.2
Find proteins for O78756 (Ovis aries)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ND6 subunitJ175Ovis ariesMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
Find proteins for O78757 (Ovis aries)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 10 kDa subunita75Ovis ariesMutation(s): 0 
Find proteins for P25712 (Bos taurus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 13 kDa subunitb96Ovis ariesMutation(s): 0 
Find proteins for P23934 (Bos taurus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 18 kDa subunitc133Ovis ariesMutation(s): 0 
Gene Names: NDUFS4
Find proteins for W5PE07 (Ovis aries)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 39 kDa subunitd338Ovis ariesMutation(s): 0 
Gene Names: NDUFA9
Find proteins for W5PI58 (Ovis aries)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B8 subunite98Ovis ariesMutation(s): 0 
Gene Names: NDUFA2
Find proteins for W5QAH8 (Ovis aries)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B13 subunitf115Ovis ariesMutation(s): 0 
Gene Names: NDUFA5
Find proteins for W5PNX7 (Ovis aries)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B14 subunitg127Ovis ariesMutation(s): 0 
Gene Names: NDUFA6
Find proteins for W5QC06 (Ovis aries)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B14.5a subunith112Ovis ariesMutation(s): 0 
Gene Names: NDUFA7
Find proteins for W5P0I2 (Ovis aries)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B17.2 subuniti145Ovis ariesMutation(s): 0 
Find proteins for B9VGZ9 (Ovis aries)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier proteinX, j88Ovis ariesMutation(s): 0 
Gene Names: NDUFAB1
Find proteins for W5NQT7 (Ovis aries)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 42 kDa subunitk320Ovis ariesMutation(s): 0 
Gene Names: NDUFA10
Find proteins for W5QBF5 (Ovis aries)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, 15 kDa subunitl105Ovis ariesMutation(s): 0 
Gene Names: NDUFS5
Find proteins for W5QFF9 (Ovis aries)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B9 subunitm83Ovis ariesMutation(s): 0 
Gene Names: NDUFA3
Find proteins for W5NYM7 (Ovis aries)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B12 subunitn97Ovis ariesMutation(s): 0 
Gene Names: NDUFB3
Find proteins for W5Q5T4 (Ovis aries)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B14.5b subunito120Ovis ariesMutation(s): 0 
Gene Names: NDUFC2
Find proteins for W5P9Q8 (Ovis aries)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B15 subunitp128Ovis ariesMutation(s): 0 
Gene Names: NDUFB4
Find proteins for W5QF73 (Ovis aries)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B16.6 subunitq143Ovis ariesMutation(s): 0 
Find proteins for Q95KV7 (Bos taurus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B17 subunitr127Ovis ariesMutation(s): 0 
Gene Names: NDUFB6
Find proteins for W5PZE3 (Ovis aries)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B18 subunits136Ovis ariesMutation(s): 0 
Gene Names: NDUFB7
Find proteins for W5P5V3 (Ovis aries)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B22 subunitt178Ovis ariesMutation(s): 0 
Gene Names: NDUFB9
Find proteins for W5PGA3 (Ovis aries)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, AGGG subunitu72Ovis ariesMutation(s): 0 
Gene Names: NDUFB2
Find proteins for W5PVD7 (Ovis aries)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialv158Ovis ariesMutation(s): 0 
Gene Names: NDUFB8
Find proteins for W5Q1B0 (Ovis aries)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, ESSS subunitw125Ovis ariesMutation(s): 0 
Gene Names: NDUFB11
Find proteins for W5PWF1 (Ovis aries)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, KFYI subunitx49Ovis ariesMutation(s): 0 
Find proteins for Q02376 (Bos taurus)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, MNLL subunity57Ovis ariesMutation(s): 0 
Find proteins for W5QG39 (Ovis aries)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, MWFE subunitz70Ovis ariesMutation(s): 0 
Find proteins for Q02377 (Bos taurus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, PDSW subunitZ175Ovis ariesMutation(s): 0 
Gene Names: NDUFB10
Find proteins for W5Q5Y9 (Ovis aries)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, PGIV subunitY171Ovis ariesMutation(s): 0 
Gene Names: NDUFA8
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, SGDH subunitW143Ovis ariesMutation(s): 0 
Gene Names: NDUFB5
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial complex I, B14.7 subunitV119Ovis ariesMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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J, L, M, i
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PC1
Query on PC1

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A, M, N, o
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
3PE
Query on 3PE

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9, J, o
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NDP
Query on NDP

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d
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
ZMP
Query on ZMP

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j
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
 Ligand Interaction
FMN
Query on FMN

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1
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
PNS
Query on PNS

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X
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
SF4
Query on SF4

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1, 3, 6, 9
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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2, 3
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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b
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 KingdomMC_U105674180

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Refinement description
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Experimental preparation
  • Version 1.3: 2019-12-11
    Changes: Other