› 8z1v

Electron Microscopy
3.16Å resolution

Cryo-EM structure of Escherichia coli DppBCDF in the resting state

Released:
DOI: 10.2210/pdb8z1v/pdb
PDB entry 8z1v coloured by chain, front view.
PDB entry 8z1v coloured by chain, side view.
PDB entry 8z1v coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural characterization of the ABC transporter DppABCDF in Escherichia coli reveals insights into dipeptide acquisition.
Li P, Zhang M, Huang Y
PLoS Biol 23 e3003026 (2025)
PMID: 40053564
Related structures: EMD-39737

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + a dipeptide-[dipeptide-binding protein](Side 1) = ADP + phosphate + a dipeptide(Side 2) + [dipeptide-binding protein](Side 1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-284557 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Dipeptide transport system permease protein DppB Chain: A
Molecule details ›
Chain: A
Length: 339 amino acids
Theoretical weight: 37.53 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEF8 (Residues: 1-339; Coverage: 100%)
Gene names: JW3512, b3543, dppB
Sequence domains:
Dipeptide transport system permease protein DppC Chain: B
Molecule details ›
Chain: B
Length: 300 amino acids
Theoretical weight: 32.33 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEG1 (Residues: 1-300; Coverage: 100%)
Gene names: JW3511, b3542, dppC
Sequence domains:
Dipeptide transport ATP-binding protein DppD Chain: C
Dipeptide transport ATP-binding protein DppF Chain: D

Ligands and Environments

1 bound ligand:
Ligand SF4 2 x SF4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.16Å
Relevant EMDB volumes: EMD-39737
Expression system: Escherichia coli

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