6M0R

2.7A Yeast Vo state3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex.

Roh, S.H.Shekhar, M.Pintilie, G.Chipot, C.Wilkens, S.Singharoy, A.Chiu, W.

(2020) Sci Adv 6

  • DOI: 10.1126/sciadv.abb9605
  • Primary Citation of Related Structures:  
    6M0R, 6M0S

  • PubMed Abstract: 
  • Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V o proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive ...

    Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V o proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo-electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c -ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c -ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.


    Organizational Affiliation

    Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'A [auth D]158Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Membrane Entity: Yes 
UniProt
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''B [auth C]198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16PPA1YHR026W
Membrane Entity: Yes 
UniProt
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V0 assembly protein 1C [auth N]52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VOA1YGR106C
Membrane Entity: Yes 
UniProt
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit eD [auth M]71Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Membrane Entity: Yes 
UniProt
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit cE, G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
Membrane Entity: Yes 
UniProt
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YPR170W-BF [auth O]69Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPR170W-B
Membrane Entity: Yes 
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit dN [auth B]345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6YLR447CL9324.8
Membrane Entity: Yes 
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformO [auth A]825Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1YOR270C
Membrane Entity: Yes 
UniProt
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Oligosaccharides

Help

Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseP5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEE
Query on PEE

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AA [auth M] , BA [auth M] , CA [auth E] , DA [auth E] , EA [auth O] , FA [auth F] , GA [auth G] , HA [auth H] , 
AA [auth M],  BA [auth M],  CA [auth E],  DA [auth E],  EA [auth O],  FA [auth F],  GA [auth G],  HA [auth H],  IA [auth I],  JA [auth I],  KA [auth J],  LA [auth J],  MA [auth K],  NA [auth K],  OA [auth B],  PA [auth A],  Q [auth C],  QA [auth A],  R [auth C],  RA [auth A],  S [auth C],  SA [auth A],  T [auth C],  TA [auth A],  U [auth C],  V [auth C],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
EYR
Query on EYR

Download Ideal Coordinates CCD File 
VA [auth A](6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene
C40 H68
NNAMSNGZQLVMQY-GAPQENEMSA-N
 Ligand Interaction
PPV
Query on PPV

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UA [auth A]PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01GM058600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10OD021600
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019M3E5D6063865
National Science Foundation (NSF, United States)United StatesMCB-1942763
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM067887
Agence Nationale de la Recherche (ANR)FranceProteaseInAction Grant

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release