6VQC

Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of V-ATPase from the mammalian brain.

Abbas, Y.M.Wu, D.Bueler, S.A.Robinson, C.V.Rubinstein, J.L.

(2020) Science 367: 1240-1246

  • DOI: 10.1126/science.aaz2924
  • Primary Citation of Related Structures:  
    6VQJ, 6VQI, 6VQK, 6VQB, 6VQA, 6VQC, 6VQH, 6VQG, 6VQ9, 6VQ6

  • PubMed Abstract: 
  • In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates t ...

    In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a Legionella pneumophila effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit D H247Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1drCG_61537
Find proteins for Q6P503 (Rattus norvegicus)
Explore Q6P503 
Go to UniProtKB:  Q6P503
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit F L119Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1fAtp6s14Vatf
Find proteins for P50408 (Rattus norvegicus)
Explore P50408 
Go to UniProtKB:  P50408
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a isoform 1 a838Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0a1Atp6n1Vpp1
Find proteins for P25286 (Rattus norvegicus)
Explore P25286 
Go to UniProtKB:  P25286
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a b205Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0bAtp6v0b_predictedrCG_50448
Find proteins for B0K022 (Rattus norvegicus)
Explore B0K022 
Go to UniProtKB:  B0K022
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1 c463Rattus norvegicusMutation(s): 0 
Gene Names: Atp6ap1Atp6ip1Atp6s1
Find proteins for O54715 (Rattus norvegicus)
Explore O54715 
Go to UniProtKB:  O54715
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit d351Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0d1rCG_51062
Find proteins for Q5M7T6 (Rattus norvegicus)
Explore Q5M7T6 
Go to UniProtKB:  Q5M7T6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2 e81Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0e2
Find proteins for Q5EB76 (Rattus norvegicus)
Explore Q5EB76 
Go to UniProtKB:  Q5EB76
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease K f98Rattus norvegicusMutation(s): 0 
Gene Names: Rnasek
Find proteins for D3ZIM6 (Rattus norvegicus)
Explore D3ZIM6 
Go to UniProtKB:  D3ZIM6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunitghijklmnghijklmno
155Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0cAtp6cAtp6lAtpl
Find proteins for P63081 (Rattus norvegicus)
Explore P63081 
Go to UniProtKB:  P63081
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Renin receptor p350Rattus norvegicusMutation(s): 0 
Gene Names: Atp6ap2Atp6ip2
Find proteins for Q6AXS4 (Rattus norvegicus)
Explore Q6AXS4 
Go to UniProtKB:  Q6AXS4
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references