5D80

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

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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:  
    5D80, 5BW9

  • 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 wilkenss@upstate.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit AABCabc617Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA1
EC: 3.6.3.14 (PDB Primary Data), 3.1 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V1-ATPase in auto-inhibited state by cryo-EM
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit BDEFdef517Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA2VAT2YBR127CYBR1002
EC: 3.6.3.14
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit HHh478Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA13CLS11YPR036WYP3085.02
EC: 3.6.3.14
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V1-ATPase in auto-inhibited state by cryo-EM
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit GJLNjln122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA10YHR039C-AYHR039BCYHR039C-B
EC: 3.6.3.14
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit EIKMikm233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA4VAT5YOR332WO6241
EC: 3.6.3.14
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Complete V1-ATPase in auto-inhibited state by cryo-EM
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit DGg256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA8YEL051WSYGP-ORF11
EC: 3.6.3.14
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit FOo118Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA7YGR020C
EC: 3.6.3.14
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 468.02α = 90
b = 159.65β = 113.75
c = 248.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata scaling
AutoPROCdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM058600

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence