6VQ6

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit A A, B, C617Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1a, rCG_52629
EC: 7.1.2.2
Find proteins for D4A133 (Rattus norvegicus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit B, brain isoform D, E, F511Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1b2, Atp6b2, Vat2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P62815 (Rattus norvegicus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit C 1 G382Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1c1
Find proteins for Q5FVI6 (Rattus norvegicus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase H+-transporting V1 subunit D H247Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1d, rCG_61537
Find proteins for Q6P503 (Rattus norvegicus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit E 1 I, J, K226Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1e1
Find proteins for Q6PCU2 (Rattus norvegicus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit F L119Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v1f, Atp6s14, Vatf
Find proteins for P50408 (Rattus norvegicus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit G M, N, O118Rattus norvegicusMutation(s): 0 
Gene Names: 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Effector protein SidK Q, R, S301Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg0968
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 116 kDa subunit a isoform 1 a838Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0a1, Atp6n1, Vpp1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P25286 (Rattus norvegicus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a b205Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0b, Atp6v0b_predicted, rCG_50448
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for B0K022 (Rattus norvegicus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit S1 c463Rattus norvegicusMutation(s): 0 
Gene Names: Atp6ap1, Atp6ip1, Atp6s1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for O54715 (Rattus norvegicus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit d351Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0d1, rCG_51062
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit e 2 e81Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0e2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease K f98Rattus norvegicusMutation(s): 0 
Gene Names: Rnasek
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for D3ZIM6 (Rattus norvegicus)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase 16 kDa proteolipid subunitg, h, i, j, k, l, m, n, g,  h,  i,  j,  k,  l,  m,  n,  o
155Rattus norvegicusMutation(s): 0 
Gene Names: Atp6v0c, Atp6c, Atp6l, Atpl
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P63081 (Rattus norvegicus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Renin receptor p350Rattus norvegicusMutation(s): 0 
Gene Names: Atp6ap2, Atp6ip2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Vacuolar ATPase (V-ATPase)		Protein: 
V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for Q6AXS4 (Rattus norvegicus)
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
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C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

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