› 6yc2

X-ray diffraction
2.5Å resolution

Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0

Released:
DOI: 10.2210/pdb6yc2/pdb
Model geometry
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PDB entry 6yc2 coloured by chain, front view.
PDB entry 6yc2 coloured by chain, side view.
PDB entry 6yc2 coloured by chain, top view.
Source organism: Dokdonia eikasta
Primary publication:
Molecular mechanism of light-driven sodium pumping.
Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Büldt G, Bamberg E, Gordeliy V
OpenAccess logo Nat Commun 11 2137 (2020)
PMID: 32358514

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: 273 amino acids
Theoretical weight: 31.08 KDa
Source organism: Dokdonia eikasta
Expression system: Escherichia coli
UniProt:
  • Canonical: N0DKS8 (Residues: 3-275; Coverage: 98%)
Gene name: NaR
Sequence domains: Bacteriorhodopsin-like protein

Ligands and Environments

5 bound ligands:
Ligand NA 5 x NA
Ligand LFA 21 x LFA
Ligand OLC 5 x OLC
Ligand OLA 5 x OLA
Ligand ALA 1 x ALA
1 modified residue:
Ligand LYR 5 x LYR

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: C2221
Unit cell:
a: 135.54Å b: 240.13Å c: 138.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.163 0.188
Expression system: Escherichia coli

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Citations

5 review citations

Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins.
Inoue K. (2021)
4 more

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