[English] 日本語
Yorodumi
- PDB-5wlp: Solution structure of the pseudo-receiver domain of Atg32 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wlp
TitleSolution structure of the pseudo-receiver domain of Atg32
ComponentsAutophagy-related protein 32
KeywordsPROTEIN TRANSPORT / Atg32 / pseudo-receiver domain
Function / homologymitochondria-nucleus signaling pathway / autophagy of mitochondrion / phagophore assembly site membrane / vacuolar membrane / mitochondrial outer membrane / mitochondrion / Autophagy-related protein 32
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsXue, X. / Pellegrini, M. / Ragusa, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113132 United States
CitationJournal: Autophagy / Year: 2018
Title: A pseudo-receiver domain in Atg32 is required for mitophagy.
Authors: Xia, X. / Katzenell, S. / Reinhart, E.F. / Bauer, K.M. / Pellegrini, M. / Ragusa, M.J.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Autophagy-related protein 32


Theoretical massNumber of molelcules
Total (without water)16,7431
Polymers16,7431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8300 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Autophagy-related protein 32 / Extracellular mutant protein 37


Mass: 16742.611 Da / Num. of mol.: 1 / Fragment: pseudo-receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATG32, ECM17, YIL146C / Plasmid: 1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40458

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 15N-separated NOESY
122isotropic13D 13C-separated NOESY
133isotropic12D D2O NOESY
141isotropic22D 1H-15N HSQC
152isotropic22D 1H-13C HSQC aliphatic
162isotropic23D HN(CA)CB
172isotropic13D HNCA
182isotropic13D HNCO
192isotropic13D HN(CO)CA
1102isotropic13D CBCA(CO)NH
1112isotropic13D HBHA(CO)NH
1172isotropic13D H(CCO)NH
1162isotropic23D (H)CCH-COSY
1152isotropic23D (H)CCH-TOCSY
1143isotropic12D DQF-COSY
1133isotropic12D 1H-1H NOESY
1123isotropic12D 1H-1H TOCSY
1182isotropic13D HN(CA)CO

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1700 uM [U-15N] Atg32, 20 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM TCEP, 99% H2O, 1% D2O15N_sample99% H2O, 1% D2O
solution2620 uM [U-13C; U-15N] Atg32, 20 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM TCEP, 99% H2O, 1% D2O15N_13C_Sample99% H2O, 1% D2O
solution3370 uM Atg32, 20 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM TCEP, 100% D2OD2O_Sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMAtg32[U-15N]1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
0.2 mMTCEPnatural abundance1
620 uMAtg32[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
0.2 mMTCEPnatural abundance2
370 uMAtg32natural abundance3
20 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
0.2 mMTCEPnatural abundance3
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AscendBrukerAscend8502

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinprocessing
CARA1.9.1.2Keller and Wuthrichchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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