› 7d3u

Electron Microscopy
3Å resolution

Structure of Mrp complex from Dietzia sp. DQ12-45-1b

Released:
DOI: 10.2210/pdb7d3u/pdb
PDB entry 7d3u coloured by chain, front view.
PDB entry 7d3u coloured by chain, side view.
PDB entry 7d3u coloured by chain, top view.
Source organism: Dietzia sp. DQ12-45-1b
Primary publication:
Structure of the Dietzia Mrp complex reveals molecular mechanism of this giant bacterial sodium proton pump.
Li B, Zhang K, Nie Y, Wang X, Zhao Y, Zhang XC, Wu XL
Proc Natl Acad Sci U S A 117 31166-31176 (2020)
PMID: 33229520
Related structures: EMD-30567

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-103942 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
NADH:quinone oxidoreductase/Mrp antiporter membrane subunit domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 574 amino acids
Theoretical weight: 59.03 KDa
Source organism: Dietzia sp. DQ12-45-1b
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A221C8X0 (Residues: 1-574; Coverage: 100%)
Gene names: GJR88_00771, amnhD
Sequence domains: Proton-conducting membrane transporter
Putative monovalent cation/H antiporter subunit A Chain: A
Molecule details ›
Chain: A
Length: 958 amino acids
Theoretical weight: 100.1 KDa
Source organism: Dietzia sp. DQ12-45-1b
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A221C8X2 (Residues: 2-958; Coverage: 100%)
Gene names: GJR88_00777, amnhA
Sequence domains:
Putative monovalent cation/H antiporter subunit C Chain: C
Molecule details ›
Chain: C
Length: 137 amino acids
Theoretical weight: 14.31 KDa
Source organism: Dietzia sp. DQ12-45-1b
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A221C8X5 (Residues: 1-137; Coverage: 100%)
Gene names: GJR88_00774, amnhC
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
Monovalent Na+/H+ antiporter subunit F Chain: F
Molecule details ›
Chain: F
Length: 85 amino acids
Theoretical weight: 8.96 KDa
Source organism: Dietzia sp. DQ12-45-1b
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A221C8X7 (Residues: 1-85; Coverage: 100%)
Gene names: GJR88_00768, amnhF
Sequence domains: Multiple resistance and pH regulation protein F (MrpF / PhaF)
Monovalent Na+/H+ antiporter subunit G Chain: G
Molecule details ›
Chain: G
Length: 125 amino acids
Theoretical weight: 12.78 KDa
Source organism: Dietzia sp. DQ12-45-1b
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A221C8Y4 (Residues: 1-125; Coverage: 100%)
Gene names: GJR88_00766, amnhG
Sequence domains: Na+/H+ antiporter subunit
Cation antiporter Chain: E
Molecule details ›
Chain: E
Length: 121 amino acids
Theoretical weight: 13.88 KDa
Source organism: Dietzia sp. DQ12-45-1b
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A221C8X1 (Residues: 1-121; Coverage: 100%)
Gene names: GJR88_00770, amnhE
Sequence domains: Na+/H+ ion antiporter subunit

Ligands and Environments

1 bound ligand:
Ligand LMT 28 x LMT
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-30567
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Structure of respiratory complex I - An emerging blueprint for the mechanism.
Kampjut et al. (2022)
2 more

2 mentions without citation

CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2.
Shor et al. (2024)
1 more