› 3wgu

X-ray diffraction
2.8Å resolution

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state without oligomycin

Released:
DOI: 10.2210/pdb3wgu/pdb
PDB entry 3wgu coloured by chain, front view.
PDB entry 3wgu coloured by chain, side view.
PDB entry 3wgu coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
Crystal structure of a Na1-bound Na1,K1-ATPase preceding the E1P state
Kanai R, Ogawa H, Vilsen B, Cornelius F, Toyoshima C
Nature 502 201-206 (2013)

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + Na(+)(Side 1) + K(+)(Side 2) = ADP + phosphate + Na(+)(Side 2) + K(+)(Side 1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138328 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Sodium/potassium-transporting ATPase subunit alpha-1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 1016 amino acids
Theoretical weight: 112.4 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P05024 (Residues: 6-1021; Coverage: 100%)
Gene name: ATP1A1
Sequence domains:
Structure domains:
Sodium/potassium-transporting ATPase subunit beta-1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 303 amino acids
Theoretical weight: 35.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P05027 (Residues: 1-303; Coverage: 100%)
Gene name: ATP1B1
Sequence domains: Sodium / potassium ATPase beta chain
Structure domains: Na, k-atpase alpha subunit.
FXYD domain-containing ion transport regulator Chains: E, G
Molecule details ›
Chains: E, G
Length: 65 amino acids
Theoretical weight: 7.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q58K79 (Residues: 1-65; Coverage: 100%)
Gene name: FXYD2
Sequence domains: ATP1G1/PLM/MAT8 family

Ligands and Environments

7 bound ligands:
Ligand MG 4 x MG
Ligand ALF 2 x ALF
Ligand ADP 2 x ADP
Ligand NA 8 x NA
Ligand CLR 6 x CLR
Ligand PC1 10 x PC1
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 106.383Å b: 211.6Å c: 257.124Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.266 0.264 0.299

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