› 8ab6

Electron Microscopy
2Å resolution

Complex III2 from Yarrowia lipolytica, combined datasets, consensus refinement

Released:
DOI: 10.2210/pdb8ab6/pdb
PDB entry 8ab6 coloured by chain, front view.
PDB entry 8ab6 coloured by chain, side view.
PDB entry 8ab6 coloured by chain, top view.
Source organism: Yarrowia lipolytica
Primary publication:
Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III2 by cryo-EM.
Wieferig JP, Kühlbrandt W
IUCrJ 10 27-37 (2023)
PMID: 36598500
Related structures: EMD-15312

Function and Biology Details

Reactions catalysed: 
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
Release of N-terminal targeting peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-179430 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Cytochrome b Chains: C, N
Molecule details ›
Chains: C, N
Length: 385 amino acids
Theoretical weight: 43.41 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D0 (Residues: 1-385; Coverage: 100%)
Gene names: COB, CYTB
Sequence domains:
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: E, P
Molecule details ›
Chains: E, P
Length: 225 amino acids
Theoretical weight: 24.56 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CI02 (Residues: 1-225; Coverage: 100%)
Gene name: YALI0_A02915g
Sequence domains:
Cytochrome b-c1 complex subunit 7 Chains: G, R
Molecule details ›
Chains: G, R
Length: 128 amino acids
Theoretical weight: 14.68 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C3K7 (Residues: 1-128; Coverage: 100%)
Gene names: QCR7, YALI0E34037g
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Ubiquinol-cytochrome C reductase hinge domain-containing protein Chains: F, Q
Molecule details ›
Chains: F, Q
Length: 137 amino acids
Theoretical weight: 15.79 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C0H4 (Residues: 1-137; Coverage: 100%)
Gene name: YALI0_F24673g
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
mitochondrial processing peptidase Chains: A, L
Molecule details ›
Chains: A, L
Length: 474 amino acids
Theoretical weight: 52.85 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CGY9 (Residues: 1-474; Coverage: 100%)
Gene name: YALI0_A14806g
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: B, M
Molecule details ›
Chains: B, M
Length: 417 amino acids
Theoretical weight: 44.28 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C2E3 (Residues: 1-417; Coverage: 100%)
Gene names: QCR2, YALI0F08613g
Sequence domains:
quinol--cytochrome-c reductase Chains: D, O
Molecule details ›
Chains: D, O
Length: 330 amino acids
Theoretical weight: 36.56 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CGP7 (Residues: 1-330; Coverage: 100%)
Gene name: YALI0_A17468g
Sequence domains: Cytochrome C1 family
Cytochrome b-c1 complex subunit 8 Chains: H, S
Molecule details ›
Chains: H, S
Length: 93 amino acids
Theoretical weight: 10.46 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C387 (Residues: 1-93; Coverage: 100%)
Gene name: YALI0_F01771g
Sequence domains: UcrQ family
Complex III subunit 9 Chains: I, T
Molecule details ›
Chains: I, T
Length: 69 amino acids
Theoretical weight: 8.04 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CG23 (Residues: 1-69; Coverage: 100%)
Gene name: YALI0_B01540g
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Cytochrome b-c1 complex subunit 10 Chains: J, U
Molecule details ›
Chains: J, U
Length: 82 amino acids
Theoretical weight: 9.11 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CC60 (Residues: 1-82; Coverage: 100%)
Gene name: YALI0_C12210g
Sequence domains: Ubiquinol-cytochrome-c reductase complex subunit (QCR10)

Ligands and Environments

7 bound ligands:
Ligand HEM 4 x HEM
Ligand PC1 4 x PC1
Ligand PTY 4 x PTY
Ligand CDL 10 x CDL
Ligand LMT 4 x LMT
Ligand XP4 2 x XP4
Ligand HEC 2 x HEC
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2Å
Relevant EMDB volumes: EMD-15312

Quick links

Citations

2 mentions without citation

Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III2 by cryo-EM.
Wieferig et al. (2023)
1 more