[English] 日本語
Yorodumi
- PDB-1pgy: Solution structure of the UBA domain in Saccharomyces cerevisiae ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pgy
TitleSolution structure of the UBA domain in Saccharomyces cerevisiae protein, Swa2p
ComponentsSwa2p
KeywordsPROTEIN BINDING / UBA / ubiquitin / Swa2 / auxilin / ubiquitin-associated domain
Function / homology
Function and homology information


endoplasmic reticulum inheritance / clathrin coat disassembly / clathrin-dependent endocytosis / clathrin binding / ubiquitin binding / vesicle / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / cytosol
Similarity search - Function
SWA2-like, ubiquitin-associated domain / Ubiquitin-associated / Ubiquitin-associated (UBA) domain / Chaperone J-domain superfamily / UBA-like superfamily / TPR repeat region circular profile. / Helicase, Ruva Protein; domain 3 / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily ...SWA2-like, ubiquitin-associated domain / Ubiquitin-associated / Ubiquitin-associated (UBA) domain / Chaperone J-domain superfamily / UBA-like superfamily / TPR repeat region circular profile. / Helicase, Ruva Protein; domain 3 / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Auxilin-like clathrin uncoating factor SWA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics
AuthorsChim, N. / Gall, W.E. / Xiao, J. / Harris, M.P. / Graham, T.R. / Krezel, A.M.
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004
Title: Solution structure of the ubiquitin-binding domain in Swa2p from Saccharomyces cerevisiae.
Authors: Chim, N. / Gall, W.E. / Xiao, J. / Harris, M.P. / Graham, T.R. / Krezel, A.M.
History
DepositionMay 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Swa2p


Theoretical massNumber of molelcules
Total (without water)5,5471
Polymers5,5471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Swa2p / auxilin-like protein


Mass: 5547.265 Da / Num. of mol.: 1 / Fragment: Ubiquitin-associated (UBA) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWA2 / Plasmid: pET32-EkLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06677

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1442D NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM UBA domain; 50mM phosphate buffer90% H2O/10% D2O
21mM UBA domain U-15N; 50mM phosphate buffer90% H2O/10% D2O
31mM UBA domain U-15N,13C; 50mM phosphate buffer90% H2O/10% D2O
41mM UBA domain; 50mM phosphate buffer100% D2O
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 6 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
CYANA1.0.6Guentert, P., Mumenthaler, C. & Wuethrich, K.structure solution
Amber7Case D.A., Pearlman D.A., Caldwell, J.W,. Cheatham T.E., Wang J., Ross W.S., Simmerling C., Darden T., Merz K.M., Stanton R.V., Cheng A., Vincent J.J., Crowley M., Tsui V., Gohlke H., Radmer R., Duan Y., Pitera J., Massova I., Seibel G.L., Singh U.C., Weiner P., Kollman P.A.refinement
XEASY1.3.xCh. Bartels, T.-H. Xia, M. Billeter, P. Guentert and K. Wuethrichdata analysis
Felix2000Accelrysdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: 373 NOE-derived distance constraints, 34 residual dipolar couplings
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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