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: 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 ...

    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 LengthOrganismDetailsImage
Mitochondrial complex I, 51 kDa subunitA [auth 1]445Ovis ariesMutation(s): 0 
Gene Names: NDUFV1
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for W5PUX0 (Ovis aries)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 24 kDa subunitB [auth 2]217Ovis ariesMutation(s): 0 
Gene Names: NDUFV2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 75 kDa subunitC [auth 3]704Ovis ariesMutation(s): 0 
Gene Names: NDUFS1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 49 kDa subunitD [auth 4]412Ovis ariesMutation(s): 0 
Gene Names: NDUFS2
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 30 kDa subunitE [auth 5]228Ovis ariesMutation(s): 0 
Gene Names: NDUFS3
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, PSST subunitF [auth 6]179Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, TYKY subunitG [auth 9]176Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND1 subunitH318Ovis ariesMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O78747 (Ovis aries)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND2 subunitI [auth N]347Ovis ariesMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND3 subunitJ [auth A]115Ovis ariesMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND4 subunitK [auth M]459Ovis ariesMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND4L subunitL [auth K]98Ovis ariesMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND5 subunitM [auth L]599Ovis ariesMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ND6 subunitN [auth J]175Ovis ariesMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 10 kDa subunitO [auth a]75Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 13 kDa subunitP [auth b]96Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 18 kDa subunitQ [auth c]133Ovis ariesMutation(s): 0 
Gene Names: NDUFS4
Membrane Entity: Yes 
UniProt
Find proteins for W5PE07 (Ovis aries)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 39 kDa subunitR [auth d]338Ovis ariesMutation(s): 0 
Gene Names: NDUFA9
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B8 subunitS [auth e]98Ovis ariesMutation(s): 0 
Gene Names: NDUFA2
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B13 subunitT [auth f]115Ovis ariesMutation(s): 0 
Gene Names: NDUFA5
Membrane Entity: Yes 
UniProt
Find proteins for W5PNX7 (Ovis aries)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B14 subunitU [auth g]127Ovis ariesMutation(s): 0 
Gene Names: NDUFA6
Membrane Entity: Yes 
UniProt
Find proteins for W5QC06 (Ovis aries)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5a subunitV [auth h]112Ovis ariesMutation(s): 0 
Gene Names: NDUFA7
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B17.2 subunitW [auth i]145Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B9VGZ9 (Ovis aries)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinQA [auth X], X [auth j]88Ovis ariesMutation(s): 0 
Gene Names: NDUFAB1
UniProt
Find proteins for W5NQT7 (Ovis aries)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 42 kDa subunitY [auth k]320Ovis ariesMutation(s): 0 
Gene Names: NDUFA10
UniProt
Find proteins for W5QBF5 (Ovis aries)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, 15 kDa subunitZ [auth l]105Ovis ariesMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B9 subunitAA [auth m]83Ovis ariesMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
UniProt
Find proteins for W5NYM7 (Ovis aries)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B12 subunitBA [auth n]97Ovis ariesMutation(s): 0 
Gene Names: NDUFB3
Membrane Entity: Yes 
UniProt
Find proteins for W5Q5T4 (Ovis aries)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.5b subunitCA [auth o]120Ovis ariesMutation(s): 0 
Gene Names: NDUFC2
Membrane Entity: Yes 
UniProt
Find proteins for W5P9Q8 (Ovis aries)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B15 subunitDA [auth p]128Ovis ariesMutation(s): 0 
Gene Names: NDUFB4
Membrane Entity: Yes 
UniProt
Find proteins for W5QF73 (Ovis aries)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B16.6 subunitEA [auth q]143Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B17 subunitFA [auth r]127Ovis ariesMutation(s): 0 
Gene Names: NDUFB6
Membrane Entity: Yes 
UniProt
Find proteins for W5PZE3 (Ovis aries)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B18 subunitGA [auth s]136Ovis ariesMutation(s): 0 
Gene Names: NDUFB7
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B22 subunitHA [auth t]178Ovis ariesMutation(s): 0 
Gene Names: NDUFB9
Membrane Entity: Yes 
UniProt
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, AGGG subunitIA [auth u]72Ovis ariesMutation(s): 0 
Gene Names: NDUFB2
Membrane Entity: Yes 
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialJA [auth v]158Ovis ariesMutation(s): 0 
Gene Names: NDUFB8
Membrane Entity: Yes 
UniProt
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, ESSS subunitKA [auth w]125Ovis ariesMutation(s): 0 
Gene Names: NDUFB11
Membrane Entity: Yes 
UniProt
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, KFYI subunitLA [auth x]49Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, MNLL subunitMA [auth y]57Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, MWFE subunitNA [auth z]70Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, PDSW subunitOA [auth Z]175Ovis ariesMutation(s): 0 
Gene Names: NDUFB10
Membrane Entity: Yes 
UniProt
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, PGIV subunitPA [auth Y]171Ovis ariesMutation(s): 0 
Gene Names: NDUFA8
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, SGDH subunitRA [auth W]143Ovis ariesMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial complex I, B14.7 subunitSA [auth V]119Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
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
 Ligand Interaction
PC1 (Subject of Investigation/LOI)
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
 Ligand Interaction
3PE (Subject of Investigation/LOI)
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
 Ligand Interaction
NDP (Subject of Investigation/LOI)
Query on NDP

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LB [auth d]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
ZMP (Subject of Investigation/LOI)
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
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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UA [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
PNS (Subject of Investigation/LOI)
Query on PNS

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

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

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

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KB [auth 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  (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