› 9brr

Electron Microscopy
4.5Å resolution

Intact V-ATPase State 3 in synaptophysin knock-out isolated synaptic vesicles

Released:
DOI: 10.2210/pdb9brr/pdb
PDB entry 9brr coloured by chain, front view.
PDB entry 9brr coloured by chain, side view.
PDB entry 9brr 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-44841

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-273834 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
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 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
V-type proton ATPase catalytic subunit A Chains: 0, 1, 2
Molecule details ›
Chains: 0, 1, 2
Length: 617 amino acids
Theoretical weight: 68.4 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P50516 (Residues: 1-617; Coverage: 100%)
Gene names: Atp6a1, Atp6a2, Atp6v1a, Atp6v1a1
Sequence domains:
V-type proton ATPase subunit B, brain isoform Chains: 3, 4, 5
Molecule details ›
Chains: 3, 4, 5
Length: 511 amino acids
Theoretical weight: 56.61 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P62814 (Residues: 1-511; Coverage: 100%)
Gene names: Atp6b2, Atp6v1b2, Vat2
Sequence domains:
V-type proton ATPase subunit D Chain: 7
Molecule details ›
Chain: 7
Length: 247 amino acids
Theoretical weight: 28.42 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P57746 (Residues: 1-247; Coverage: 100%)
Gene names: Atp6m, Atp6v1d, Vatd
Sequence domains: ATP synthase subunit D
V-type proton ATPase subunit E 1 Chains: 8, 9, Q
Molecule details ›
Chains: 8, 9, Q
Length: 226 amino acids
Theoretical weight: 26.2 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P50518 (Residues: 1-226; Coverage: 100%)
Gene names: Atp6e, Atp6e2, Atp6v1e1
Sequence domains: ATP synthase (E/31 kDa) subunit
V-type proton ATPase subunit G 2 Chains: R, T, V
Molecule details ›
Chains: R, T, V
Length: 118 amino acids
Theoretical weight: 13.67 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9WTT4 (Residues: 1-118; Coverage: 100%)
Gene names: Atp6g2, Atp6v1g2, Ng38
Sequence domains: Vacuolar (H+)-ATPase G subunit
V-type proton ATPase subunit F Chain: X
Molecule details ›
Chain: X
Length: 119 amino acids
Theoretical weight: 13.39 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D1K2 (Residues: 1-119; Coverage: 100%)
Gene names: Atp6s14, Atp6v1f, Vatf
Sequence domains: ATP synthase (F/14-kDa) subunit
V-type proton ATPase subunit C 1 Chain: 6
Molecule details ›
Chain: 6
Length: 382 amino acids
Theoretical weight: 43.95 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9Z1G3 (Residues: 1-382; Coverage: 100%)
Gene names: Atp6c, Atp6c1, Atp6v1c1, Vatc
Sequence domains: V-ATPase subunit C
V-type proton ATPase subunit H Chain: U
Molecule details ›
Chain: U
Length: 483 amino acids
Theoretical weight: 55.92 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8BVE3 (Residues: 1-483; Coverage: 100%)
Gene name: Atp6v1h
Sequence domains:
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
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
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
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 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:
Renin receptor Chain: p
Molecule details ›
Chain: p
Length: 350 amino acids
Theoretical weight: 39.13 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CYN9 (Residues: 1-350; Coverage: 100%)
Gene names: Atp6ap2, Atp6ip2
Sequence domains: Renin receptor-like protein

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-44841

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