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Electron Microscopy
3Å resolution

The Vo region of human V-ATPase in state 1 (focused refinement)

Released:
Source organism: Homo sapiens
Primary publication:
Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Mol Cell 80 501-511.e3 (2020)
PMID: 33065002
Related structures: EMD-21844

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-127434 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (12 distinct):
V-type proton ATPase 21 kDa proteolipid subunit c'' Chain: 0
Molecule details ›
Chain: 0
Length: 205 amino acids
Theoretical weight: 21.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99437 (Residues: 1-205; Coverage: 100%)
Gene names: ATP6F, ATP6V0B
Sequence domains: ATP synthase subunit C
V-type proton ATPase 16 kDa proteolipid subunit c Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9
Molecule details ›
Chains: 1, 2, 3, 4, 5, 6, 7, 8, 9
Length: 155 amino acids
Theoretical weight: 15.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P27449 (Residues: 1-155; Coverage: 100%)
Gene names: ATP6C, ATP6L, ATP6V0C, ATPL
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit d 1 Chain: Q
Molecule details ›
Chain: Q
Length: 351 amino acids
Theoretical weight: 40.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61421 (Residues: 1-351; Coverage: 100%)
Gene names: ATP6D, ATP6V0D1, VPATPD
Sequence domains: ATP synthase (C/AC39) subunit
V-type proton ATPase 116 kDa subunit a 1 Chain: R
Molecule details ›
Chain: R
Length: 837 amino acids
Theoretical weight: 96.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q93050 (Residues: 1-837; Coverage: 100%)
Gene names: ATP6N1, ATP6N1A, ATP6V0A1, VPP1
Sequence domains: V-type ATPase 116kDa subunit family
V-type proton ATPase subunit e 1 Chain: S
Molecule details ›
Chain: S
Length: 81 amino acids
Theoretical weight: 9.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15342 (Residues: 1-81; Coverage: 100%)
Gene names: ATP6H, ATP6V0E, ATP6V0E1
Sequence domains: ATP synthase subunit H
Ribonuclease kappa Chain: T
Molecule details ›
Chain: T
Length: 137 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P5S7 (Residues: 1-137; Coverage: 100%)
Gene name: RNASEK
V-type proton ATPase subunit S1 Chain: U
Molecule details ›
Chain: U
Length: 470 amino acids
Theoretical weight: 52.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15904 (Residues: 1-470; Coverage: 100%)
Gene names: ATP6AP1, ATP6IP1, ATP6S1, VATPS1, XAP3
Sequence domains:
Renin receptor Chain: V
Molecule details ›
Chain: V
Length: 350 amino acids
Theoretical weight: 39.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75787 (Residues: 1-350; Coverage: 100%)
Gene names: ATP6AP2, ATP6IP2, CAPER, ELDF10, HT028, MSTP009, PSEC0072
Sequence domains: Renin receptor-like protein

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GLC
Carbohydrate polymer : NEW Components: BGC, GAL, NGA, SIA
Carbohydrate polymer : NEW Components: GAL, NGA, SIA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution:
Relevant EMDB volumes: EMD-21844