› 7u4t

Electron Microscopy
3.6Å resolution

Human V-ATPase in state 2 with SidK and mEAK-7

Released:
DOI: 10.2210/pdb7u4t/pdb
PDB entry 7u4t coloured by chain, front view.
PDB entry 7u4t coloured by chain, side view.
PDB entry 7u4t coloured by chain, top view.
Source organisms:
Primary publication:
Identification of mEAK-7 as a human V-ATPase regulator via cryo-EM data mining.
Wang L, Wu D, Robinson CV, Fu TM
OpenAccess logo Proc Natl Acad Sci U S A 119 e2203742119 (2022)
PMID: 35994636
Related structures: EMD-26334

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-518506 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
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 C 1 Chain: O
Molecule details ›
Chain: O
Length: 382 amino acids
Theoretical weight: 44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P21283 (Residues: 1-382; Coverage: 100%)
Gene names: ATP6C, ATP6D, ATP6V1C1, VATC
Sequence domains: V-ATPase subunit C
V-type proton ATPase subunit E 1 Chains: H, I, J
Molecule details ›
Chains: H, I, J
Length: 226 amino acids
Theoretical weight: 26.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P36543 (Residues: 1-226; Coverage: 100%)
Gene names: ATP6E, ATP6E2, ATP6V1E1
Sequence domains: ATP synthase (E/31 kDa) subunit
V-type proton ATPase subunit G 1 Chains: K, L, M
Molecule details ›
Chains: K, L, M
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75348 (Residues: 1-118; Coverage: 100%)
Gene names: ATP6G, ATP6G1, ATP6J, ATP6V1G1
Sequence domains: Vacuolar (H+)-ATPase G subunit
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
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 catalytic subunit A Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 617 amino acids
Theoretical weight: 68.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P38606 (Residues: 1-617; Coverage: 100%)
Gene names: ATP6A1, ATP6V1A, ATP6V1A1, VPP2
Sequence domains:
V-type proton ATPase subunit B, brain isoform Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 511 amino acids
Theoretical weight: 56.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P21281 (Residues: 1-511; Coverage: 100%)
Gene names: ATP6B2, ATP6V1B2, VPP3
Sequence domains:
Type IV secretion protein Dot Chains: X, Y, Z
Molecule details ›
Chains: X, Y, Z
Length: 573 amino acids
Theoretical weight: 65.51 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5ZWW6 (Residues: 1-573; Coverage: 100%)
Gene name: lpg0968
V-type proton ATPase subunit D Chain: G
Molecule details ›
Chain: G
Length: 247 amino acids
Theoretical weight: 28.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y5K8 (Residues: 1-247; Coverage: 100%)
Gene names: ATP6M, ATP6V1D, VATD
Sequence domains: ATP synthase subunit D
V-type proton ATPase subunit F Chain: N
Molecule details ›
Chain: N
Length: 119 amino acids
Theoretical weight: 13.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16864 (Residues: 1-119; Coverage: 100%)
Gene names: ATP6S14, ATP6V1F, VATF
Sequence domains: ATP synthase (F/14-kDa) subunit
V-type proton ATPase subunit H Chain: P
Molecule details ›
Chain: P
Length: 483 amino acids
Theoretical weight: 55.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UI12 (Residues: 1-483; Coverage: 100%)
Gene names: ATP6V1H, CGI-11
Sequence domains:
MTOR-associated protein MEAK7 Chain: W
Molecule details ›
Chain: W
Length: 456 amino acids
Theoretical weight: 51.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q6P9B6 (Residues: 1-456; Coverage: 100%)
Gene names: KIAA1609, MEAK7, TLDC1
Sequence domains: TLD

Ligands and Environments

2 bound ligands:
Ligand NAG 8 x NAG
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-26334
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Targeting of lysosomal-bound protein mEAK-7 for cancer therapy.
Chang et al. (2024)
5 other articles

1 mention without citation

Structure and topography of the synaptic V-ATPase-synaptophysin complex.
Wang et al. (2024)