6VQA

Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1126/science.aaz2924
  • Primary Citation of Related Structures:  
    6VQ6, 6VQ7, 6VQ8, 6VQ9, 6VQA, 6VQB, 6VQC, 6VQG, 6VQH, 6VQI, 6VQJ, 6VQK

  • 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.


  • Organizational Affiliation

    Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit A
A, B, C
617Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for D4A133 (Rattus norvegicus)
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UniProt GroupD4A133
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoform
D, E, F
511Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P62815 (Rattus norvegicus)
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UniProt GroupP62815
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit DG [auth H]247Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6P503 (Rattus norvegicus)
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UniProt GroupQ6P503
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1H [auth I],
I [auth J],
J [auth K]
226Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6PCU2 (Rattus norvegicus)
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UniProt GroupQ6PCU2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit GK [auth M],
L [auth N],
M [auth O]
118Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q8R2H0 (Rattus norvegicus)
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Effector protein SidKN [auth Q],
O [auth R],
P [auth S]
301Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg0968
UniProt
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
Q [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
R [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references