[English] 日本語
Yorodumi
- PDB-7fda: CryoEM Structure of Reconstituted V-ATPase, state1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fda
TitleCryoEM Structure of Reconstituted V-ATPase, state1
Components
  • (V-type proton ATPase subunit ...) x 11
  • (Yeast Vacuolar ATPase ...) x 3
  • Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)
  • V0 assembly protein 1
KeywordsMOTOR PROTEIN / ATPase / proton pump / rotary motor enzyme / membrane protein
Function / homology
Function and homology information


Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH ...Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / synaptic vesicle lumen acidification / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane / lysosomal lumen acidification / pexophagy / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / protein targeting to vacuole / vacuole organization / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / ROS and RNS production in phagocytes / cellular hyperosmotic response / Nef Mediated CD4 Down-regulation / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / regulation of macroautophagy / enzyme regulator activity / ATP metabolic process / Insulin receptor recycling / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / endosome membrane / membrane raft / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily ...ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / ATPase, V1 complex, subunit B / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / 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-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / 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 D / V-type proton ATPase subunit c' ...V-type proton ATPase subunit f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / 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 D / V-type proton ATPase subunit c' / V-type proton ATPase subunit F / V-type proton ATPase subunit H / V0 assembly protein 1 / V-type proton ATPase subunit e / V-type proton ATPase subunit H
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKhan, M.M. / Lee, S. / Oot, R.A. / Couoh-Cardel, S. / KIm, H. / Wilkens, S. / Roh, S.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM058600 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA228340 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
CitationJournal: EMBO J / Year: 2022
Title: Oxidative stress protein Oxr1 promotes V-ATPase holoenzyme disassembly in catalytic activity-independent manner.
Authors: Md Murad Khan / Seowon Lee / Sergio Couoh-Cardel / Rebecca A Oot / Hyunmin Kim / Stephan Wilkens / Soung-Hun Roh /
Abstract: The vacuolar ATPase (V-ATPase) is a rotary motor proton pump that is regulated by an assembly equilibrium between active holoenzyme and autoinhibited V -ATPase and V proton channel subcomplexes. ...The vacuolar ATPase (V-ATPase) is a rotary motor proton pump that is regulated by an assembly equilibrium between active holoenzyme and autoinhibited V -ATPase and V proton channel subcomplexes. Here, we report cryo-EM structures of yeast V-ATPase assembled in vitro from lipid nanodisc reconstituted V and mutant V . Our analysis identified holoenzymes in three active rotary states, indicating that binding of V to V provides sufficient free energy to overcome V autoinhibition. Moreover, the structures suggest that the unequal spacing of V 's proton-carrying glutamic acid residues serves to alleviate the symmetry mismatch between V and V motors, a notion that is supported by mutagenesis experiments. We also uncover a structure of free V bound to Oxr1, a conserved but poorly characterized factor involved in the oxidative stress response. Biochemical experiments show that Oxr1 inhibits V -ATPase and causes disassembly of the holoenzyme, suggesting that Oxr1 plays a direct role in V-ATPase regulation.
History
DepositionJul 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-31538
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Yeast Vacuolar ATPase A subunit
B: V-type proton ATPase subunit B
C: Yeast Vacuolar ATPase A subunit
D: V-type proton ATPase subunit B
E: Yeast Vacuolar ATPase A subunit
F: V-type proton ATPase subunit B
G: V-type proton ATPase subunit E
H: V-type proton ATPase subunit G
I: V-type proton ATPase subunit E
J: V-type proton ATPase subunit G
K: V-type proton ATPase subunit E
L: V-type proton ATPase subunit G
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
O: V-type proton ATPase subunit C
P: Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)
Q: Yeast Vacuolar ATPase a subunit
S: V-type proton ATPase subunit d
T: V-type proton ATPase subunit c''
U: V-type proton ATPase subunit c'
V: V-type proton ATPase subunit c
W: V-type proton ATPase subunit c
X: V-type proton ATPase subunit c
Y: V-type proton ATPase subunit c
Z: V-type proton ATPase subunit c
a: V-type proton ATPase subunit c
b: V-type proton ATPase subunit c
c: V-type proton ATPase subunit c
d: V-type proton ATPase subunit e
e: V0 assembly protein 1
f: Yeast Vacuolar ATPase f subunit


Theoretical massNumber of molelcules
Total (without water)991,82531
Polymers991,82531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Concanamycin A sensitive MgATPase activity
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area128820 Å2
ΔGint-973 kcal/mol
Surface area354180 Å2

-
Components

-
Yeast Vacuolar ATPase ... , 3 types, 5 molecules ACEQf

#1: Protein Yeast Vacuolar ATPase A subunit


Mass: 67796.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
#9: Protein Yeast Vacuolar ATPase a subunit


Mass: 95625.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32563
#16: Protein Yeast Vacuolar ATPase f subunit


Mass: 9369.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P0C5R9

-
V-type proton ATPase subunit ... , 11 types, 24 molecules BDFGIKHJLMNOSTUVWXYZabcd

#2: Protein V-type proton ATPase subunit B / V-ATPase subunit B


Mass: 57815.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P16140
#3: Protein V-type proton ATPase subunit E / V-ATPase subunit E


Mass: 26508.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P22203
#4: Protein V-type proton ATPase subunit G


Mass: 13735.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
#5: Protein V-type proton ATPase subunit D / V-ATPase subunit D


Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32610
#6: Protein V-type proton ATPase subunit F / V-ATPase subunit F


Mass: 13479.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39111
#7: Protein V-type proton ATPase subunit C / V-ATPase subunit C


Mass: 44241.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P31412
#10: Protein V-type proton ATPase subunit d / V-ATPase subunit d


Mass: 39822.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32366
#11: Protein V-type proton ATPase subunit c'' / V-ATPase subunit c''


Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P23968
#12: Protein V-type proton ATPase subunit c' / V-ATPase subunit c'


Mass: 17046.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32842
#13: Protein
V-type proton ATPase subunit c / V-ATPase subunit c


Mass: 16357.501 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P25515
#14: Protein V-type proton ATPase subunit e / V-ATPase subunit e


Mass: 8387.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q3E7B6

-
Protein , 2 types, 2 molecules Pe

#8: Protein Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) / V-ATPase subunit H


Mass: 53885.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Homo sapiens (human)
Strain: S288c / Gene: ATP6V1H / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P41807, UniProt: Q9UI12
#15: Protein V0 assembly protein 1


Mass: 29694.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P53262

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Yeast Vacuolar ATPase in rotary state 1COMPLEXall0MULTIPLE SOURCES
2Yeast V-type proton ATPase subunit CCOMPLEX#71RECOMBINANT
3Chimeric subunit HCOMPLEX#81RECOMBINANTFusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)
4V-type proton ATPase subunitsCOMPLEX#1-#6, #9-#161NATURALV-ATPase subunits purified from natural source
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Saccharomyces cerevisiae S288c (yeast)559292
22Saccharomyces cerevisiae S288c (yeast)559292
32Homo sapiens (human)9606
43Saccharomyces cerevisiae S288c (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
22Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 85109
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

SoftwareName: PHENIX / Version: 1.19rc6_4061: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
7Cootmodel fitting
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85109 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00365666
ELECTRON MICROSCOPYf_angle_d0.51888844
ELECTRON MICROSCOPYf_dihedral_angle_d4.5528920
ELECTRON MICROSCOPYf_chiral_restr0.03910243
ELECTRON MICROSCOPYf_plane_restr0.00311334

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more