› 9bry

Electron Microscopy
3.6Å resolution

V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles

Released:
DOI: 10.2210/pdb9bry/pdb
PDB entry 9bry coloured by chain, front view.
PDB entry 9bry coloured by chain, side view.
PDB entry 9bry coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure and topography of the synaptic V-ATPase-synaptophysin complex.
Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held R, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT
Nature (2024)
PMID: 38838737
Related structures: EMD-44845

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-246058 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (10 distinct):
V-type proton ATPase subunit S1 Chain: c
Molecule details ›
Chain: c
Length: 463 amino acids
Theoretical weight: 51.05 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9R1Q9 (Residues: 1-463; Coverage: 100%)
Gene names: Atp6ap1, Atp6ip1, Atp6s1
Sequence domains:
V-type proton ATPase 21 kDa proteolipid subunit c'' Chain: b
Molecule details ›
Chain: b
Length: 205 amino acids
Theoretical weight: 21.62 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q91V37 (Residues: 1-205; Coverage: 100%)
Gene names: Atp6f, Atp6v0b
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit d 1 Chain: d
Molecule details ›
Chain: d
Length: 351 amino acids
Theoretical weight: 40.34 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P51863 (Residues: 1-351; Coverage: 100%)
Gene names: Atp6d, Atp6v0d1
Sequence domains: ATP synthase (C/AC39) subunit
Ribonuclease kappa Chain: f
Molecule details ›
Chain: f
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8K3C0 (Residues: 1-98; Coverage: 100%)
Gene names: D11Bwg0434e, Rnasek
V-type proton ATPase 16 kDa proteolipid subunit c Chains: g, h, i, j, k, l, m, n, o
Molecule details ›
Chains: g, h, i, j, k, l, m, n, o
Length: 155 amino acids
Theoretical weight: 15.82 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P63082 (Residues: 1-155; Coverage: 100%)
Gene names: Atp6c, Atp6l, Atp6v0c, Atpl, Mvp
Sequence domains: ATP synthase subunit C
Renin receptor extracellular fragment Chain: p
Molecule details ›
Chain: p
Length: 290 amino acids
Theoretical weight: 32.75 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CYN9 (Residues: 61-350; Coverage: 87%)
Gene names: Atp6ap2, Atp6ip2
Sequence domains: Renin receptor-like protein
V-type proton ATPase subunit e 2 Chain: e
Molecule details ›
Chain: e
Length: 81 amino acids
Theoretical weight: 9.2 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q91XE7 (Residues: 1-81; Coverage: 100%)
Gene name: Atp6v0e2
Sequence domains: ATP synthase subunit H
V-type proton ATPase 116 kDa subunit a 1 Chain: a
Molecule details ›
Chain: a
Length: 838 amino acids
Theoretical weight: 96.44 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9Z1G4 (Residues: 1-838; Coverage: 100%)
Gene names: Atp6n1, Atp6v0a1
Sequence domains: V-type ATPase 116kDa subunit family

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 4 x NAG
Ligand BMA 1 x BMA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-44845

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