› 8j5t

Electron Microscopy
2.98Å resolution

Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state

Released:
DOI: 10.2210/pdb8j5t/pdb
PDB entry 8j5t coloured by chain, front view.
PDB entry 8j5t coloured by chain, side view.
PDB entry 8j5t coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B
Nat Struct Mol Biol (2024)
PMID: 38548954
Related structures: EMD-35993

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-242610 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Uncharacterized protein Rv1280c Chain: A
Molecule details ›
Chain: A
Length: 599 amino acids
Theoretical weight: 64.5 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: P9WGU5 (Residues: 1-591; Coverage: 100%)
Gene names: MTCY50.02, Rv1280c
Sequence domains: Bacterial extracellular solute-binding proteins, family 5 Middle
Putative peptide transport permease protein Rv1283c Chain: B
Molecule details ›
Chain: B
Length: 325 amino acids
Theoretical weight: 35.12 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: P9WFZ7 (Residues: 1-325; Coverage: 100%)
Gene names: MTCY373.02c, Rv1283c
Sequence domains:
Putative peptide transport permease protein Rv1282c Chain: C
Molecule details ›
Chain: C
Length: 291 amino acids
Theoretical weight: 31.4 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: P9WFZ9 (Residues: 1-291; Coverage: 100%)
Gene names: MTCY373.01c, MTCY3H3.01, Rv1282c
Sequence domains:
Uncharacterized ABC transporter ATP-binding protein Rv1281c Chain: D
Molecule details ›
Chain: D
Length: 612 amino acids
Theoretical weight: 65.34 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: P9WQJ5 (Residues: 1-612; Coverage: 100%)
Gene names: MTCY50.01, Rv1281c
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 2 x MG
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.98Å
Relevant EMDB volumes: EMD-35993
Expression system: Mycolicibacterium smegmatis MC2 155

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