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 1.4 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: https://doi.org/10.1038/nature19794
  • Primary Citation of Related Structures:  
    5LNK

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 51 kDa subunitA [auth 1]445Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PUX0 (Ovis aries)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 24 kDa subunitB [auth 2]217Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5NRY1 (Ovis aries)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 75 kDa subunitC [auth 3]704Ovis ariesMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 49 kDa subunitD [auth 4]412Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5PJ73 (Ovis aries)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 30 kDa subunitE [auth 5]228Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5PB27 (Ovis aries)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, PSST subunitF [auth 6]179Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, TYKY subunitG [auth 9]176Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND1 subunit318Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78747 (Ovis aries)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND2 subunitI [auth N]347Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78748 (Ovis aries)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND3 subunitJ [auth A]115Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78753 (Ovis aries)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND4 subunitK [auth M]459Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78755 (Ovis aries)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND4L subunitL [auth K]98Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78754 (Ovis aries)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND5 subunitM [auth L]599Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78756 (Ovis aries)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ND6 subunitN [auth J]175Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O78757 (Ovis aries)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 10 kDa subunitO [auth a]75Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 13 kDa subunitP [auth b]96Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 18 kDa subunitQ [auth c]133Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PE07 (Ovis aries)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 39 kDa subunitR [auth d]338Ovis ariesMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B8 subunitS [auth e]98Ovis ariesMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B13 subunitT [auth f]115Ovis ariesMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B14 subunitU [auth g]127Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5QC06 (Ovis aries)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5a subunitV [auth h]112Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P0I2 (Ovis aries)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B17.2 subunitW [auth i]145Ovis ariesMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinQA [auth X],
X [auth j]
88Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5NQT7 (Ovis aries)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 42 kDa subunitY [auth k]320Ovis ariesMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, 15 kDa subunitZ [auth l]105Ovis ariesMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B9 subunitAA [auth m]83Ovis ariesMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B12 subunitBA [auth n]97Ovis ariesMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5b subunitCA [auth o]120Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P9Q8 (Ovis aries)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B15 subunitDA [auth p]128Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5QF73 (Ovis aries)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B16.6 subunitEA [auth q]143Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B17 subunitFA [auth r]127Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PZE3 (Ovis aries)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B18 subunitGA [auth s]136Ovis ariesMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B22 subunitHA [auth t]178Ovis ariesMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, AGGG subunitIA [auth u]72Ovis ariesMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialJA [auth v]158Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5Q1B0 (Ovis aries)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, ESSS subunitKA [auth w]125Ovis ariesMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, KFYI subunitLA [auth x]49Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, MNLL subunitMA [auth y]57Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, MWFE subunitNA [auth z]70Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, PDSW subunitOA [auth Z]175Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5Q5Y9 (Ovis aries)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, PGIV subunitPA [auth Y]171Ovis ariesMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, SGDH subunitRA [auth W]143Ovis ariesMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.7 subunitSA [auth V]119Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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GB [auth M],
HB [auth L],
IB [auth J],
MB [auth i]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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DB [auth N],
EB [auth A],
FB [auth M],
OB [auth o]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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AB [auth 9],
JB [auth J],
PB [auth o],
QB [auth o]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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LB [auth d]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZMP
Query on ZMP

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NB [auth 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
FMN
Query on FMN

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UA [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
PNS
Query on PNS

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RB [auth X]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
SF4
Query on SF4

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BB [auth 9]
CB [auth 9]
TA [auth 1]
WA [auth 3]
XA [auth 3]
BB [auth 9],
CB [auth 9],
TA [auth 1],
WA [auth 3],
XA [auth 3],
ZA [auth 6]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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VA [auth 2],
YA [auth 3]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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KB [auth b]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX

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  (Full details and data files)

  • 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
  • Version 1.4: 2021-06-02
    Changes: Derived calculations