› 3x3b

X-ray diffraction
2.3Å resolution

Crystal structure of the light-driven sodium pump KR2 in acidic state

Released:
DOI: 10.2210/pdb3x3b/pdb
PDB entry 3x3b coloured by chain, front view.
PDB entry 3x3b coloured by chain, side view.
PDB entry 3x3b coloured by chain, top view.
Source organism: Dokdonia eikasta
Primary publication:
Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump.
Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, Nureki O
Nature 521 48-53 (2015)
PMID: 25849775

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-126093 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sodium pumping rhodopsin Chain: A
Molecule details ›
Chain: A
Length: 290 amino acids
Theoretical weight: 32.89 KDa
Source organism: Dokdonia eikasta
Expression system: Escherichia coli
UniProt:
  • Canonical: N0DKS8 (Residues: 1-275; Coverage: 98%)
Gene name: NaR
Sequence domains: Bacteriorhodopsin-like protein
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

3 bound ligands:
Ligand RET 1 x RET
Ligand OLA 3 x OLA
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: I222
Unit cell:
a: 40.582Å b: 81.544Å c: 233.775Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.207 0.249
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Silencing Neurons: Tools, Applications, and Experimental Constraints.
Wiegert et al. (2017)
18 more

9 mentions without citation

Conversion of microbial rhodopsins: insights into functionally essential elements and rational protein engineering.
Kaneko et al. (2017)
8 more