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- PDB-6m0s: 3.6A Yeast Vo state3 prime -

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Basic information

Entry
Database: PDB / ID: 6m0s
Title3.6A Yeast Vo state3 prime
Components
  • (V-type proton ATPase subunit ...) x 6
  • Uncharacterized protein YPR170W-B
  • V0 assembly protein 1
KeywordsTRANSPORT PROTEIN / V-ATPase / Vo sub-complex / rotary motor
Function / homology
Function and homology information


cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / protein localization to vacuolar membrane / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / protein localization to vacuolar membrane / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar proton-transporting V-type ATPase complex / cellular hyperosmotic response / vacuolar acidification / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / proton-transporting ATPase activity, rotational mechanism / intracellular copper ion homeostasis / Neutrophil degranulation / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum membrane / membrane
Similarity search - Function
: / V-type proton ATPase subunit f-like / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic ...: / V-type proton ATPase subunit f-like / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type proton ATPase subunit f / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit c' / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRoh, S.H. / Shekhar, M. / Pintilie, G. / Chipot, C. / Wilkens, S. / SIngharoy, A. / Chiu, W.
Funding support United States, Korea, Republic Of, France, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM058600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD021600 United States
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063865 Korea, Republic Of
National Science Foundation (NSF, United States)MCB-1942763 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM067887 United States
Agence Nationale de la Recherche (ANR)ProteaseInAction Grant France
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V complex.
Authors: Soung-Hun Roh / Mrinal Shekhar / Grigore Pintilie / Christophe Chipot / Stephan Wilkens / Abhishek Singharoy / Wah Chiu /
Abstract: Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, ...Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V 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 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 that shows the -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 -ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.
History
DepositionFeb 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 4, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: V-type proton ATPase subunit a, vacuolar isoform
M: V-type proton ATPase subunit e
O: Uncharacterized protein YPR170W-B
B: V-type proton ATPase subunit d
C: V-type proton ATPase subunit c''
D: V-type proton ATPase subunit c'
E: V-type proton ATPase subunit c
F: V-type proton ATPase subunit c
G: V-type proton ATPase subunit c
H: V-type proton ATPase subunit c
I: V-type proton ATPase subunit c
J: V-type proton ATPase subunit c
K: V-type proton ATPase subunit c
L: V-type proton ATPase subunit c
N: V0 assembly protein 1


Theoretical massNumber of molelcules
Total (without water)322,86915
Polymers322,86915
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area57350 Å2
ΔGint-625 kcal/mol
Surface area112670 Å2

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Components

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V-type proton ATPase subunit ... , 6 types, 13 molecules AMBCDEFGHIJKL

#1: Protein V-type proton ATPase subunit a, vacuolar isoform / V-ATPase a 1 subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1 / Vacuolar proton pump a ...V-ATPase a 1 subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1 / Vacuolar proton pump a subunit / Vacuolar proton translocating ATPase subunit a 1


Mass: 94289.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VPH1, YOR270C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32563
#2: Protein V-type proton ATPase subunit e / V-ATPase subunit e / Low dye-binding protein 10 / Vacuolar proton pump subunit e


Mass: 8186.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VMA9, CWH36, LDB10, YCL005W-A / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7B6
#4: Protein V-type proton ATPase subunit d / V-ATPase subunit d / V-ATPase 39 kDa subunit / V-ATPase subunit M39 / Vacuolar proton pump subunit d


Mass: 39822.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VMA6, YLR447C, L9324.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32366
#5: Protein V-type proton ATPase subunit c'' / V-ATPase subunit c'' / V-ATPase 22 kDa proteolipid subunit / Vacuolar proton pump c'' subunit


Mass: 20880.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VMA16, PPA1, YHR026W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23968
#6: Protein V-type proton ATPase subunit c' / V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase ...V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase 16 kDa proteolipid subunit 2 / Vacuolar proton pump c' subunit


Mass: 16414.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VMA11, CLS9, TFP3, YPL234C, P1064 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32842
#7: Protein
V-type proton ATPase subunit c / V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / ...V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / Vacuolar proton pump c subunit


Mass: 16254.358 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VMA3, CLS7, CUP5, GEF2, YEL027W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25515

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Protein , 2 types, 2 molecules ON

#3: Protein Uncharacterized protein YPR170W-B


Mass: 7487.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YPR170W-B / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C5R9
#8: Protein V0 assembly protein 1


Mass: 5752.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VOA1, YGR106C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53262

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: V-type proton ATPase Vo sub-complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 400 kDa/nm / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2744: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28726 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00345106
ELECTRON MICROSCOPYf_angle_d0.65981656
ELECTRON MICROSCOPYf_dihedral_angle_d10.38817872
ELECTRON MICROSCOPYf_chiral_restr0.0393639
ELECTRON MICROSCOPYf_plane_restr0.0036592

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