[English] 日本語
Yorodumi
- PDB-6hh0: Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hh0
TitleYeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles
ComponentsV-type proton ATPase subunit a, vacuolar isoform
KeywordsMEMBRANE PROTEIN / ATPasse / transmembrane helix / DPC micelle / NMR spectroscopy
Function / homology
Function and homology information


protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / cellular hyperosmotic response ...protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / cellular hyperosmotic response / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-3,5-bisphosphate binding / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transport / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / ATPase binding / protein-containing complex assembly / membrane raft
Similarity search - Function
ATPase, V0 complex, subunit 116kDa, eukaryotic / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family
Similarity search - Domain/homology
V-type proton ATPase subunit a, vacuolar isoform
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsZangger, K. / Hohlweg, W. / Wagner, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A cation-pi interaction in a transmembrane helix of vacuolar ATPase retains the proton-transporting arginine in a hydrophobic environment.
Authors: Hohlweg, W. / Wagner, G.E. / Hofbauer, H.F. / Sarkleti, F. / Setz, M. / Gubensak, N. / Lichtenegger, S. / Falsone, S.F. / Wolinski, H. / Kosol, S. / Oostenbrink, C. / Kohlwein, S.D. / Zangger, K.
History
DepositionAug 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V-type proton ATPase subunit a, vacuolar isoform


Theoretical massNumber of molelcules
Total (without water)2,8321
Polymers2,8321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2660 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide 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: 2832.328 Da / Num. of mol.: 1 / Fragment: transmembrane helix 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPH1, YOR270C / Production host: synthetic construct (others) / References: UniProt: P32563

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic13D NOESY-N-HSQC
141isotropic12D HSQC
151isotropic13D NOESY C-HSQC

-
Sample preparation

DetailsType: micelle
Contents: 100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O
Details: 100 mM deuterated DPC 50 mM KPi pH 5.0 / Label: partially 13C, 15N double labeled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMDeuterated DPC[U-99% 2H]1
50 mMpotassium phosphatenone1
0.02 %sodium azidenone1
1 mMTM7 peptide13C and 15N labeled aminoacids 8 and 121
Sample conditionsIonic strength: 50 mM / Label: condition / pH: 5.0 / Pressure: ambient atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

+
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://pdbjlvh1.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