› 7jrp

Electron Microscopy
3.8Å resolution

Plant Mitochondrial complex SC III2+IV from Vigna radiata

Released:
DOI: 10.2210/pdb7jrp/pdb
PDB entry 7jrp coloured by chain, front view.
PDB entry 7jrp coloured by chain, side view.
PDB entry 7jrp coloured by chain, top view.
Source organisms:
Primary publication:
Atomic structures of respiratory complex III2, complex IV, and supercomplex III2-IV from vascular plants.
Maldonado M, Guo F, Letts JA
Elife 10 (2021)
PMID: 33463523
Related structures: EMD-22448

Function and Biology Details

Reactions catalysed: 
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
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 30-mer (preferred)
PDBe Complex ID:
PDB-CPX-103680 (preferred)
Entry contents:
20 distinct polypeptide molecules
Macromolecules (20 distinct):
Probable mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 Chains: A, M
Molecule details ›
Chains: A, M
Length: 527 amino acids
Theoretical weight: 58.71 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3TWG4 (Residues: 1-527; Coverage: 100%)
Gene name: LOC106759431
Sequence domains:
Mitochondrial-processing peptidase subunit alpha Chains: B, N
Molecule details ›
Chains: B, N
Length: 506 amino acids
Theoretical weight: 54.54 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3VF71 (Residues: 1-506; Coverage: 100%)
Gene name: LOC106774328
Sequence domains:
COB Chains: C, O
Molecule details ›
Chains: C, O
Length: 393 amino acids
Theoretical weight: 44.35 KDa
Source organism: Vigna radiata
Cytochrome c domain-containing protein Chains: D, P
Molecule details ›
Chains: D, P
Length: 306 amino acids
Theoretical weight: 33.56 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3W199 (Residues: 1-306; Coverage: 100%)
Gene name: LOC106780282
Sequence domains: Cytochrome C1 family
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: E, Q
Molecule details ›
Chains: E, Q
Length: 271 amino acids
Theoretical weight: 30.05 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3TB49 (Residues: 1-271; Coverage: 100%)
Gene name: LOC106753663
Sequence domains:
Cytochrome b-c1 complex subunit 7 Chains: F, R
Molecule details ›
Chains: F, R
Length: 122 amino acids
Theoretical weight: 14.39 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3U9J1 (Residues: 1-122; Coverage: 100%)
Gene name: LOC106763052
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Cytochrome b-c1 complex subunit 8 Chains: G, S
Molecule details ›
Chains: G, S
Length: 72 amino acids
Theoretical weight: 8.35 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3U9S5 (Residues: 1-72; Coverage: 100%)
Gene name: LOC106763113
Sequence domains: Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit 6 Chains: H, T
Molecule details ›
Chains: H, T
Length: 69 amino acids
Theoretical weight: 8.12 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3VHC0 (Residues: 1-69; Coverage: 100%)
Gene name: LOC106775083
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Complex III subunit 9 Chains: J, V
Molecule details ›
Chains: J, V
Length: 72 amino acids
Theoretical weight: 8.2 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3TQD2 (Residues: 1-72; Coverage: 100%)
Gene name: LOC106757742
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
QCR10 Chains: K, W
Molecule details ›
Chains: K, W
Length: 81 amino acids
Theoretical weight: 8.95 KDa
Source organism: Vigna radiata
COX1 Chain: a
Molecule details ›
Chain: a
Length: 527 amino acids
Theoretical weight: 57.96 KDa
Source organism: Vigna radiata
Cytochrome c oxidase subunit 2 Chain: b
Molecule details ›
Chain: b
Length: 251 amino acids
Theoretical weight: 28.39 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3TZB2 (Residues: 133-383; Coverage: 66%)
Gene name: LOC106760164
Sequence domains:
COX3 Chain: c
Molecule details ›
Chain: c
Length: 265 amino acids
Theoretical weight: 29.97 KDa
Source organism: Vigna radiata
COX4 Chain: d
Molecule details ›
Chain: d
Length: 79 amino acids
Theoretical weight: 8.81 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3TNX9 (Residues: 46-124; Coverage: 64%)
Gene name: LOC106757297
Sequence domains: Protein of unknown function (DUF1138)
Cytochrome c oxidase subunit 5b-2, mitochondrial Chain: e
Molecule details ›
Chain: e
Length: 150 amino acids
Theoretical weight: 16.69 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3U1E4 (Residues: 1-150; Coverage: 100%)
Gene name: LOC106760900
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 6a, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 100 amino acids
Theoretical weight: 11.23 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3UMA0 (Residues: 1-100; Coverage: 100%)
Gene name: LOC106766916
Sequence domains: Cytochrome c oxidase subunit VIa
Cytochrome c oxidase subunit 6b-1 Chain: g
Molecule details ›
Chain: g
Length: 181 amino acids
Theoretical weight: 20.02 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3VV60 (Residues: 1-181; Coverage: 100%)
Gene name: LOC106778794
Sequence domains: Cytochrome oxidase c subunit VIb
Cytochrome c oxidase subunit 5C Chain: h
Molecule details ›
Chain: h
Length: 64 amino acids
Theoretical weight: 7.12 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3V319 (Residues: 1-64; Coverage: 100%)
Gene name: LOC106771138
COX7a Chain: i
Molecule details ›
Chain: i
Length: 67 amino acids
Theoretical weight: 7.62 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3TUX2 (Residues: 1-67; Coverage: 100%)
Gene name: LOC106759053
Sequence domains: Cytochrome c oxidase subunit VII
SLL1 protein Chain: j
Molecule details ›
Chain: j
Length: 96 amino acids
Theoretical weight: 10.51 KDa
Source organism: Vigna radiata var. radiata
UniProt:
  • Canonical: A0A1S3V7C2 (Residues: 1-96; Coverage: 100%)
Gene name: LOC106772338

Ligands and Environments

11 bound ligands:
Ligand ZN 3 x ZN
Ligand PC1 5 x PC1
Ligand CDL 9 x CDL
Ligand HEM 4 x HEM
Ligand 3PE 29 x 3PE
Ligand HEC 2 x HEC
Ligand HEA 2 x HEA
Ligand CU 1 x CU
Ligand MG 1 x MG
Ligand CUA 1 x CUA
Ligand LYS 1 x LYS
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-22448

Quick links

Citations

5 review citations

The functional significance of mitochondrial respiratory chain supercomplexes.
Kohler et al. (2023)
4 more

3 mentions without citation

The biogenesis and regulation of the plant oxidative phosphorylation system.
Ghifari et al. (2023)
2 more