6O7V

Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural comparison of the vacuolar and Golgi V-ATPases fromSaccharomyces cerevisiae.

Vasanthakumar, T.Bueler, S.A.Wu, D.Beilsten-Edmands, V.Robinson, C.V.Rubinstein, J.L.

(2019) Proc Natl Acad Sci U S A 116: 7272-7277

  • DOI: 10.1073/pnas.1814818116
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are diffe ...

    Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast Saccharomyces cerevisiae , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V O complexes containing Stv1p could be readily purified without attached V 1 regions. We used this effect to determine structures of the membrane-embedded V O region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V O region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.


    Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit DM256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA8YEL051WSYGP-ORF11
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit GH, J, L114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA10YHR039C-AYHR039BCYHR039C-B
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit EG, I, K233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA4VAT5YOR332WO6241
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit HP478Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA13CLS11YPR036WYP3085.02
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit CO392Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA5VAT3VATCYKL080WYKL410
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, Golgi isoforma890Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STV1YMR054WYM9796.07
Find proteins for P37296 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
V0 assembly protein 1b265Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''c213Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit dd345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6YLR447CL9324.8
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit cg, h, i, j, k, l, m, n160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'o164Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit ee73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Putative protein YPR170W-Bf85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPR170W-B
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit FN118Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA7YGR020C
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vacuolar ATP synthase catalytic subunit AA, C, E639Saccharomyces cerevisiae RM11-1aMutation(s): 0 
Gene Names: SCRG_00677
Find proteins for B3LH69 (Saccharomyces cerevisiae (strain RM11-1a))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit BB, D, F517Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA2VAT2YBR127CYBR1002
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP81294

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-15
    Changes: Author supporting evidence