Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A6B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 259.96 kDa 
• Atom Count: 5278 
• Residue Count: 1062 
• Unique protein chains: 4

6VQI

Mammalian V-ATPase from rat brain collar and peripheral stalks rotational state 1 (from focused refinement)

• DOI: 10.2210/pdb6VQI/pdb
• EMDataResource: EMD-21351

• Classification: PROTON TRANSPORT
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2020-02-05 Released: 2020-03-18 
• Deposition Author(s): Abbas, Y.M., Rubinstein, J.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 32165585 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C 1	G	382	Rattus norvegicus	Mutation(s): 0  Gene Names: Atp6v1c1
Find proteins for Q5FVI6 (Rattus norvegicus) Explore Q5FVI6  Go to UniProtKB:  Q5FVI6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit E 1	I, J, K	226	Rattus norvegicus	Mutation(s): 0  Gene Names: Atp6v1e1
Find proteins for Q6PCU2 (Rattus norvegicus) Explore Q6PCU2  Go to UniProtKB:  Q6PCU2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit G	M, N, O	118	Rattus norvegicus	Mutation(s): 0  Gene Names:  Atp6v1g2, Aif1, Bat1a, Cdk2ap1-ps2, Cdk2ap1-ps3, Cdk2ap1-ps4, Cdk2ap1-ps5, Cdk2ap1-ps6, E230034O05Rik, LOC224733l-3, LOC224733l-4, LOC224733l-5, LOC224733l-6, LOC224733l-7, LOC224733l-8, Lst1, RT1-CE12, RT1-CE3, RT1-CE5, RT1-CE6, RT1-CE8, RT1-CE9, Sacm2l-ps3, Sacm2l-ps4, Sacm2l-ps5, Sacm2l-ps6, Sacm2l-ps7, Tnf, rCG_38311
Find proteins for Q8R2H0 (Rattus norvegicus) Explore Q8R2H0  Go to UniProtKB:  Q8R2H0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a isoform 1	a	838	Rattus norvegicus	Mutation(s): 0  Gene Names: Atp6v0a1, Atp6n1, Vpp1
Find proteins for P25286 (Rattus norvegicus) Explore P25286  Go to UniProtKB:  P25286

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-05 
• Released Date: 2020-03-18 
Deposition Author(s): Abbas, Y.M., Rubinstein, J.L.

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Funding Organization	Location	Grant 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