› 6tk7

X-ray diffraction
1.6Å resolution

Femtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in acidic conditions

Released:
DOI: 10.2210/pdb6tk7/pdb
PDB entry 6tk7 coloured by chain, front view.
PDB entry 6tk7 coloured by chain, side view.
PDB entry 6tk7 coloured by chain, top view.
Source organism: Dokdonia eikasta
Primary publication:
Femtosecond-to-millisecond structural changes in a light-driven sodium pump.
Skopintsev P, Ehrenberg D, Weinert T, James D, Kar RK, Johnson PJM, Ozerov D, Furrer A, Martiel I, Dworkowski F, Nass K, Knopp G, Cirelli C, Arrell C, Gashi D, Mous S, Wranik M, Gruhl T, Kekilli D, Brünle S, Deupi X, Schertler GFX, Benoit RM, Panneels V, Nogly P, Schapiro I, Milne C, Heberle J, Standfuss J
Nature 583 314-318 (2020)
PMID: 32499654

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
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

Ligands and Environments

2 bound ligands:
Ligand RET 1 x RET
Ligand LFA 26 x LFA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SwissFEL ARAMIS BEAMLINE ESA
Spacegroup: I222
Unit cell:
a: 41.54Å b: 84.48Å c: 235.56Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.213
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Using azobenzene photocontrol to set proteins in motion.
Bozovic et al. (2022)
10 more

3 mentions without citation

Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser.
Yun et al. (2021)
2 more