6O7W

Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 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
  • Primary Citation of Related Structures:  

  • 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

    Physical and Theoretical Chemistry Laboratory, University of Oxford, OX1 3QZ Oxford, United Kingdom.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; john.rubinstein@utoronto.ca.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit D
M
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA8
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32610
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit F
N
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA7
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39111
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vacuolar ATP synthase catalytic subunit A
C, E, A
639Saccharomyces cerevisiae (strain RM11-1a)Mutation(s): 0 
Find proteins for B3LH69 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3LH69
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit B
D, F, B
517Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA2 (VAT2)
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16140
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit G
L, H, J
114Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA10
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48836
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit E
K, G, I
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA4 (VAT5)
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22203
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit H
P
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA13 (CLS11)
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41807
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit C
O
392Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA5 (VAT3, VATC)
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P31412
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, Golgi isoform
a
890Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: STV1
Find proteins for P37296 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P37296
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
V0 assembly protein 1
b
265Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VOA1
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53262
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''
c
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA16 (PPA1)
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23968
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit d
d
345Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA6
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32366
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c
g, h, i, j, k, l, m, n
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA3 (CLS7, CUP5, GEF2)
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25515
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'
o
164Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA11 (CLS9, TFP3)
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32842
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit e
e
73Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA9 (CWH36, LDB10)
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7B6
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Putative protein YPR170W-B
f
85Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C5R9
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-04-24
    Type: Data collection, Database references
  • Version 1.3: 2020-01-15
    Type: Author supporting evidence