› 5d3m

X-ray diffraction
3.3Å resolution

Folate ECF transporter: AMPPNP bound state

Released:
DOI: 10.2210/pdb5d3m/pdb
PDB entry 5d3m coloured by chain, front view.
PDB entry 5d3m coloured by chain, side view.
PDB entry 5d3m coloured by chain, top view.
Source organism: Lactobacillus delbrueckii
Primary publication:
Structural insight in the toppling mechanism of an energy-coupling factor transporter.
Swier LJ, Guskov A, Slotboom DJ
Nat Commun 7 11072 (2016)
PMID: 27026363

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-172828 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Energy-coupling factor transporter ATP-binding protein EcfA1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 298 amino acids
Theoretical weight: 32.91 KDa
Source organism: Lactobacillus delbrueckii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q1GBJ0 (Residues: 2-280; Coverage: 99%)
Gene names: Ldb0424, cbiO1, ecfA1
Sequence domains: ABC transporter
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Energy-coupling factor transporter ATP-binding protein EcfA2 Chains: B, F
Molecule details ›
Chains: B, F
Length: 287 amino acids
Theoretical weight: 31.67 KDa
Source organism: Lactobacillus delbrueckii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q1GBI9 (Residues: 1-287; Coverage: 100%)
Gene names: Ldb0425, cbiO2, ecfA2
Sequence domains: ABC transporter
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Conserved hypothetical membrane protein Chains: C, G
Molecule details ›
Chains: C, G
Length: 184 amino acids
Theoretical weight: 20.48 KDa
Source organism: Lactobacillus delbrueckii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q1G929 (Residues: 1-176; Coverage: 100%)
Gene name: Ldb1625
Sequence domains: ECF transporter, substrate-specific component
Structure domains: Arp2/3 complex 21 kDa subunit ARPC3
Energy-coupling factor transporter transmembrane protein EcfT Chains: D, H
Molecule details ›
Chains: D, H
Length: 265 amino acids
Theoretical weight: 30.29 KDa
Source organism: Lactobacillus delbrueckii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q1GBI8 (Residues: 1-265; Coverage: 100%)
Gene names: Ldb0426, cbiQ, ecfT
Sequence domains: Cobalt transport protein

Ligands and Environments

1 bound ligand:
Ligand ANP 4 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 90.07Å b: 97.26Å c: 105.45Å
α: 84.67° β: 64.78° γ: 62.59°
R-values:
R R work R free
0.252 0.25 0.289
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Mechanism of Action of ABC Importers: Conservation, Divergence, and Physiological Adaptations.
Lewinson et al. (2017)
4 more

5 mentions without citation

Structural and functional diversity calls for a new classification of ABC transporters.
Thomas et al. (2020)
4 more