5D80

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.202 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of yeast V1-ATPase in the autoinhibited state.

Oot, R.A.Kane, P.M.Berry, E.A.Wilkens, S.

(2016) Embo J. 35: 1694-1706

  • DOI: 10.15252/embj.201593447
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vacuolar ATPases (V-ATPases) are essential proton pumps that acidify the lumen of subcellular organelles in all eukaryotic cells and the extracellular space in some tissues. V-ATPase activity is regulated by a unique mechanism referred to as reversib ...

    Vacuolar ATPases (V-ATPases) are essential proton pumps that acidify the lumen of subcellular organelles in all eukaryotic cells and the extracellular space in some tissues. V-ATPase activity is regulated by a unique mechanism referred to as reversible disassembly, wherein the soluble catalytic sector, V1, is released from the membrane and its MgATPase activity silenced. The crystal structure of yeast V1 presented here shows that activity silencing involves a large conformational change of subunit H, with its C-terminal domain rotating ~150° from a position near the membrane in holo V-ATPase to a position at the bottom of V1 near an open catalytic site. Together with biochemical data, the structure supports a mechanistic model wherein subunit H inhibits ATPase activity by stabilizing an open catalytic site that results in tight binding of inhibitory ADP at another site.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA wilkenss@upstate.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase catalytic subunit A
A, B, C, a, b, c
617Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA1 (CLS8, TFP1)
EC: 7.1.2.2
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17255
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit B
D, E, F, d, e, f
517Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA2 (VAT2)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16140
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit H
H, h
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA13 (CLS11)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41807
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit G
J, L, N, j, l, n
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA10
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48836
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit E
I, K, M, i, k, m
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA4 (VAT5)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22203
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit D
G, g
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32610
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit F
o, O
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA7
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39111
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.202 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.255 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 468.020α = 90.00
b = 159.650β = 113.75
c = 248.270γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXrefinement
Aimlessdata scaling
AutoPROCdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM058600

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description