› 6rf4

X-ray diffraction
2.4Å resolution

Crystal structure of the potassium-pumping S254A mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0

Released:
DOI: 10.2210/pdb6rf4/pdb
PDB entry 6rf4 coloured by chain, front view.
PDB entry 6rf4 coloured by chain, side view.
PDB entry 6rf4 coloured by chain, top view.
Source organism: Dokdonia eikasta
Primary publication:
Structure and mechanisms of sodium-pumping KR2 rhodopsin.
Kovalev K, Polovinkin V, Gushchin I, Alekseev A, Shevchenko V, Borshchevskiy V, Astashkin R, Balandin T, Bratanov D, Vaganova S, Popov A, Chupin V, Büldt G, Bamberg E, Gordeliy V
Sci Adv 5 eaav2671 (2019)
PMID: 30989112

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126095 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sodium pumping rhodopsin Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 288 amino acids
Theoretical weight: 32.6 KDa
Source organism: Dokdonia eikasta
Expression system: Escherichia coli
UniProt:
  • Canonical: N0DKS8 (Residues: 1-280; Coverage: 100%)
Gene name: NaR
Sequence domains: Bacteriorhodopsin-like protein
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

5 bound ligands:
Ligand OLC 25 x OLC
Ligand LFA 29 x LFA
Ligand NA 5 x NA
Ligand BOG 5 x BOG
Ligand RET 5 x RET
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: C2221
Unit cell:
a: 131.396Å b: 240.045Å c: 135.14Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.212
Expression system: Escherichia coli

Quick links

Citations

7 review citations

New era of optogenetics: from the central to peripheral nervous system.
Xu et al. (2020)
6 more