› 5j4z

Electron Microscopy
5.8Å resolution

Architecture of tight respirasome

Released:
DOI: 10.2210/pdb5j4z/pdb
PDB 5j4z coloured by chain and viewed from the front.
PDB 5j4z coloured by chain and viewed from the side.
PDB 5j4z coloured by chain and viewed from the top.
Source organism: Ovis aries
Primary publication:
The architecture of respiratory supercomplexes.
Letts JA, Fiedorczuk K, Sazanov LA
Nature 537 644-648 (2016)
PMID: 27654913
Related structures: EMD-8130

Function and Biology Details

Reaction catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 89-mer (preferred)
Entry contents:
74 distinct polypeptide molecules
Macromolecules (74 distinct):
COMPLEX I ND3 Chain: A
Molecule details ›
Chain: A
Length: 102 amino acids
Theoretical weight: 8.7 KDa
Source organism: Ovis aries
COMPLEX I PSST/NDUFS7 Chain: B
Molecule details ›
Chain: B
Length: 154 amino acids
Theoretical weight: 13.2 KDa
Source organism: Ovis aries
COMPLEX I 30KDA/NDUFS3 Chain: C
Molecule details ›
Chain: C
Length: 194 amino acids
Theoretical weight: 16.53 KDa
Source organism: Ovis aries
COMPLEX I 49KDA/NDUFS2 Chain: D
Molecule details ›
Chain: D
Length: 384 amino acids
Theoretical weight: 32.7 KDa
Source organism: Ovis aries
COMPLEX I 24KDA/NDUFV2 Chain: E
Molecule details ›
Chain: E
Length: 189 amino acids
Theoretical weight: 16.17 KDa
Source organism: Ovis aries
COMPLEX I 51KDA/NDUFV1 Chain: F
Molecule details ›
Chain: F
Length: 429 amino acids
Theoretical weight: 36.6 KDa
Source organism: Ovis aries
COMPLEX I 75KDA/NDUFS1 Chain: G
Molecule details ›
Chain: G
Length: 652 amino acids
Theoretical weight: 55.76 KDa
Source organism: Ovis aries
COMPLEX I ND1 Chain: H
Molecule details ›
Chain: H
Length: 297 amino acids
Theoretical weight: 25.29 KDa
Source organism: Ovis aries
COMPLEX I TYKY/NDUFS8 Chain: I
Molecule details ›
Chain: I
Length: 171 amino acids
Theoretical weight: 14.72 KDa
Source organism: Ovis aries
COMPLEX I ND6 Chain: J
Molecule details ›
Chain: J
Length: 171 amino acids
Theoretical weight: 14.57 KDa
Source organism: Ovis aries
COMPLEX I ND4L Chain: K
Molecule details ›
Chain: K
Length: 93 amino acids
Theoretical weight: 7.93 KDa
Source organism: Ovis aries
COMPLEX I ND5 Chain: L
Molecule details ›
Chain: L
Length: 575 amino acids
Theoretical weight: 48.95 KDa
Source organism: Ovis aries
COMPLEX I ND4 Chain: M
Molecule details ›
Chain: M
Length: 455 amino acids
Theoretical weight: 38.74 KDa
Source organism: Ovis aries
COMPLEX I ND2 Chain: N
Molecule details ›
Chain: N
Length: 345 amino acids
Theoretical weight: 29.38 KDa
Source organism: Ovis aries
COMPLEX I 18KDA/NDUFS6 Chain: O
Molecule details ›
Chain: O
Length: 104 amino acids
Theoretical weight: 8.87 KDa
Source organism: Ovis aries
COMPLEX I 13KDA/NDUFS6 Chain: P
Molecule details ›
Chain: P
Length: 85 amino acids
Theoretical weight: 7.25 KDa
Source organism: Ovis aries
COMPLEX I 15KDA/NDUFS5 Chain: Q
Molecule details ›
Chain: Q
Length: 66 amino acids
Theoretical weight: 5.63 KDa
Source organism: Ovis aries
COMPLEX I MWFE/NDUFA1 Chain: R
Molecule details ›
Chain: R
Length: 29 amino acids
Theoretical weight: 2.49 KDa
Source organism: Ovis aries
COMPLEX I B8/NDUFA2 Chains: S, d
Molecule details ›
Chains: S, d
Length: 80 amino acids
Theoretical weight: 6.83 KDa
Source organism: Ovis aries
COMPLEX I B9/NDUFA3 Chain: T
Molecule details ›
Chain: T
Length: 53 amino acids
Theoretical weight: 4.53 KDa
Source organism: Ovis aries
COMPLEX I B13/NDUFA5 Chain: U
Molecule details ›
Chain: U
Length: 96 amino acids
Theoretical weight: 8.19 KDa
Source organism: Ovis aries
COMPLEX I B14/NDUFA6 Chain: V
Molecule details ›
Chain: V
Length: 112 amino acids
Theoretical weight: 9.55 KDa
Source organism: Ovis aries
COMPLEX I PGIV/NDUFA8 Chain: W
Molecule details ›
Chain: W
Length: 103 amino acids
Theoretical weight: 8.78 KDa
Source organism: Ovis aries
COMPLEX I 39KDA/NDUFA9 Chain: X
Molecule details ›
Chain: X
Length: 309 amino acids
Theoretical weight: 26.32 KDa
Source organism: Ovis aries
COMPLEX I 42KDA/NDUFA10 Chain: Y
Molecule details ›
Chain: Y
Length: 322 amino acids
Theoretical weight: 27.42 KDa
Source organism: Ovis aries
COMPLEX I B14.7/NDUFA11 Chain: Z
Molecule details ›
Chain: Z
Length: 119 amino acids
Theoretical weight: 10.15 KDa
Source organism: Ovis aries
COMPLEX I B17.2/NDUFA12 Chain: a
Molecule details ›
Chain: a
Length: 111 amino acids
Theoretical weight: 9.46 KDa
Source organism: Ovis aries
COMPLEX I B16.6/NDUFA13 Chain: b
Molecule details ›
Chain: b
Length: 92 amino acids
Theoretical weight: 7.85 KDa
Source organism: Ovis aries
COMPLEX I SDAP/NDUFAB1 Chain: c
Molecule details ›
Chain: c
Length: 79 amino acids
Theoretical weight: 6.74 KDa
Source organism: Ovis aries
COMPLEX I SDAP/NDUFAB1 Chain: e
Molecule details ›
Chain: e
Length: 55 amino acids
Theoretical weight: 4.7 KDa
Source organism: Ovis aries
COMPLEX I SDAP/NDUFAB1 Chain: f
Molecule details ›
Chain: f
Length: 59 amino acids
Theoretical weight: 5.04 KDa
Source organism: Ovis aries
COMPLEX I B15/NDUFB4 Chain: g
Molecule details ›
Chain: g
Length: 130 amino acids
Theoretical weight: 11.08 KDa
Source organism: Ovis aries
COMPLEX I B18/NDUFB7 Chains: 9, h, z
Molecule details ›
Chains: 9, h, z
Length: 63 amino acids
Theoretical weight: 5.38 KDa
Source organism: Ovis aries
COMPLEX I B22/NDUFB9 Chain: i
Molecule details ›
Chain: i
Length: 70 amino acids
Theoretical weight: 5.98 KDa
Source organism: Ovis aries
COMPLEX I PDSW/NDUFB10 Chain: j
Molecule details ›
Chain: j
Length: 44 amino acids
Theoretical weight: 3.76 KDa
Source organism: Ovis aries
COMPLEX I ESSS/NDUFB11 Chain: k
Molecule details ›
Chain: k
Length: 83 amino acids
Theoretical weight: 7.08 KDa
Source organism: Ovis aries
COMPLEX I KFYI/NDUFC1 Chain: 0
Molecule details ›
Chain: 0
Length: 36 amino acids
Theoretical weight: 3.08 KDa
Source organism: Ovis aries
COMPLEX I B14.5B/NDUFC2 Chain: 1
Molecule details ›
Chain: 1
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 1 Chain: 2
Molecule details ›
Chain: 2
Length: 38 amino acids
Theoretical weight: 3.25 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2 Chains: 3, 4
Molecule details ›
Chains: 3, 4
Length: 28 amino acids
Theoretical weight: 2.4 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3 Chain: 5
Molecule details ›
Chain: 5
Length: 34 amino acids
Theoretical weight: 2.91 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4 Chain: 6
Molecule details ›
Chain: 6
Length: 21 amino acids
Theoretical weight: 1.81 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5 Chain: 7
Molecule details ›
Chain: 7
Length: 39 amino acids
Theoretical weight: 3.34 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6 Chain: 8
Molecule details ›
Chain: 8
Length: 27 amino acids
Theoretical weight: 2.32 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 11 Chain: y
Molecule details ›
Chain: y
Length: 46 amino acids
Theoretical weight: 3.93 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 12 Chain: x
Molecule details ›
Chain: x
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 13 Chain: w
Molecule details ›
Chain: w
Length: 24 amino acids
Theoretical weight: 2.06 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 14 Chain: v
Molecule details ›
Chain: v
Length: 18 amino acids
Theoretical weight: 1.55 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 15 Chain: u
Molecule details ›
Chain: u
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Ovis aries
COMPLEX I UNKNOWN SUBUNIT FRAGMENT 16 Chain: t
Molecule details ›
Chain: t
Length: 12 amino acids
Theoretical weight: 1.04 KDa
Source organism: Ovis aries
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: AA, AL
Molecule details ›
Chains: AA, AL
Length: 449 amino acids
Theoretical weight: 49.65 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5Q5G6 (Residues: 35-483; Coverage: 93%)
Gene name: LOC101110095
Sequence domains:
COMPLEX III SUBUNIT 2 / CORE 2 Chains: AB, AM
Molecule details ›
Chains: AB, AM
Length: 423 amino acids
Theoretical weight: 45.19 KDa
Source organism: Ovis aries
Cytochrome b Chains: AC, AN
Molecule details ›
Chains: AC, AN
Length: 378 amino acids
Theoretical weight: 42.68 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: P24959 (Residues: 2-379; Coverage: 100%)
Gene names: COB, CYTB, MT-CYB, MTCYB
Sequence domains:
COMPLEX III SUBUNIT 4 / CYTOCHROME C1 Chains: AD, AO
Molecule details ›
Chains: AD, AO
Length: 241 amino acids
Theoretical weight: 27.32 KDa
Source organism: Ovis aries
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: AE, AP
Molecule details ›
Chains: AE, AP
Length: 196 amino acids
Theoretical weight: 21.65 KDa
Source organism: Ovis aries
Cytochrome b-c1 complex subunit 7 Chains: AF, AQ
Molecule details ›
Chains: AF, AQ
Length: 105 amino acids
Theoretical weight: 12.95 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5P642 (Residues: 5-109; Coverage: 96%)
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Cytochrome b-c1 complex subunit 8 Chains: AG, AR
Molecule details ›
Chains: AG, AR
Length: 75 amino acids
Theoretical weight: 8.88 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PUP9 (Residues: 2-76; Coverage: 92%)
Gene name: LOC101121420
Sequence domains: UcrQ family
Cytochrome b-c1 complex subunit 6 Chains: AH, AS
Molecule details ›
Chains: AH, AS
Length: 67 amino acids
Theoretical weight: 7.92 KDa
Source organism: Ovis aries
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: AI, AT
Molecule details ›
Chains: AI, AT
Length: 57 amino acids
Theoretical weight: 5.82 KDa
Source organism: Ovis aries
COMPLEX III SUBUNIT 9 / 7.2KDA Chains: AJ, AU
Molecule details ›
Chains: AJ, AU
Length: 60 amino acids
Theoretical weight: 6.94 KDa
Source organism: Ovis aries
COMPLEX III SUBUNIT 10 / 6.4KDA Chains: AK, AV
Molecule details ›
Chains: AK, AV
Length: 51 amino acids
Theoretical weight: 5.93 KDa
Source organism: Ovis aries
Cytochrome c oxidase subunit 1 Chain: BN
Molecule details ›
Chain: BN
Length: 514 amino acids
Theoretical weight: 57.08 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78749 (Residues: 1-514; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c oxidase subunit 2 Chain: BO
Molecule details ›
Chain: BO
Length: 227 amino acids
Theoretical weight: 26.02 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78750 (Residues: 1-227; Coverage: 100%)
Gene names: COII, COX2, COXII, MT-CO2, MTCO2
Sequence domains:
Cytochrome c oxidase subunit 3 Chain: BC
Molecule details ›
Chain: BC
Length: 259 amino acids
Theoretical weight: 29.66 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O21619 (Residues: 3-261; Coverage: 99%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase subunit 4 Chain: BD
Molecule details ›
Chain: BD
Length: 144 amino acids
Theoretical weight: 16.9 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PPE8 (Residues: 26-169; Coverage: 85%)
Gene name: LOC101105179
Sequence domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 5A, mitochondrial Chain: BE
Molecule details ›
Chain: BE
Length: 105 amino acids
Theoretical weight: 12.08 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5NXT8 (Residues: 17-121; Coverage: 87%)
Sequence domains: Cytochrome c oxidase subunit Va
Cytochrome c oxidase subunit 5B, mitochondrial Chain: BP
Molecule details ›
Chain: BP
Length: 98 amino acids
Theoretical weight: 10.67 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PW27 (Residues: 46-143; Coverage: 69%)
Gene name: LOC101110664
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 6A, mitochondrial Chain: BG
Molecule details ›
Chain: BG
Length: 84 amino acids
Theoretical weight: 9.54 KDa
Source organism: Ovis aries
COMPLEX IV COX6B1 Chain: BH
Molecule details ›
Chain: BH
Length: 79 amino acids
Theoretical weight: 9.41 KDa
Source organism: Ovis aries
Cytochrome c oxidase subunit 6C Chain: BI
Molecule details ›
Chain: BI
Length: 73 amino acids
Theoretical weight: 8.47 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PXG3 (Residues: 2-74; Coverage: 99%)
Sequence domains: Cytochrome c oxidase subunit VIc
Cytochrome c oxidase subunit 7A1, mitochondrial Chain: BJ
Molecule details ›
Chain: BJ
Length: 58 amino acids
Theoretical weight: 6.54 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5P5H0 (Residues: 20-77; Coverage: 74%)
Gene name: LOC101121285
Sequence domains: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 7B, mitochondrial Chain: BK
Molecule details ›
Chain: BK
Length: 49 amino acids
Theoretical weight: 5.46 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5QE72 (Residues: 35-83; Coverage: 58%)
Sequence domains: Cytochrome C oxidase chain VIIB
Cytochrome c oxidase subunit 7C, mitochondrial Chain: BL
Molecule details ›
Chain: BL
Length: 46 amino acids
Theoretical weight: 5.36 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P7E5B2 (Residues: 18-63; Coverage: 73%)
Gene name: LOC114115573
Sequence domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 8 Chain: BM
Molecule details ›
Chain: BM
Length: 43 amino acids
Theoretical weight: 4.74 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PFK9 (Residues: 25-69; Coverage: 60%)
Sequence domains: Cytochrome oxidase c subunit VIII

Ligands and Environments

6 bound ligands:
Ligand SF4 6 x SF4
Ligand FES 4 x FES
Ligand HEM 6 x HEM
Ligand CU 1 x CU
Ligand HEA 2 x HEA
Ligand CUA 1 x CUA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.8Å
Relevant EMDB volumes: EMD-8130

Quick links

Citations

60 review citations

In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.
Chavez et al. (2022)
59 more

18 mentions without citation

Mitochondrial respiratory supercomplexes in mammalian cells: structural versus functional role.
Javadov et al. (2021)
17 more