[English] 日本語
Yorodumi
- PDB-1p9c: NMR solution structure of the C-terminal ubiquitin-interacting mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p9c
TitleNMR solution structure of the C-terminal ubiquitin-interacting motif of the proteasome subunit S5a
Components26S proteasome non-ATPase regulatory subunit 4
KeywordsLIGAND BINDING PROTEIN / ALPHA HELIX / HAIRPIN LOOP
Function / homology
Function and homology information


proteasome accessory complex / proteasome regulatory particle, base subcomplex / Proteasome assembly / polyubiquitin modification-dependent protein binding / proteasome complex / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA binding / nucleoplasm / identical protein binding ...proteasome accessory complex / proteasome regulatory particle, base subcomplex / Proteasome assembly / polyubiquitin modification-dependent protein binding / proteasome complex / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #120 / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / von Willebrand factor (vWF) type A domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #120 / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Helix non-globular / Special
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, T.D. / Feigon, J.
CitationJournal: Embo J. / Year: 2003
Title: Structural determinants for the binding of ubiquitin-like domains to the proteasome.
Authors: Mueller, T.D. / Feigon, J.
History
DepositionMay 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: 26S proteasome non-ATPase regulatory subunit 4


Theoretical massNumber of molelcules
Total (without water)4,9161
Polymers4,9161
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit S5A / Rpn10 / Multiubiquitin chain binding protein / ...26S proteasome regulatory subunit S5A / Rpn10 / Multiubiquitin chain binding protein / Antisecretory factor-1 / AF / ASF


Mass: 4916.343 Da / Num. of mol.: 1 / Fragment: C-terminal ubiquitin-interacting motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4 OR MCB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55036

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 13C-separated NOESY
NMR detailsText: The structure was determined using standard triple-resonance NMR spectroscopy techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM S5a peptide, unlabeled50mM sodium phosphate; 100mM sodium chloride; 5% D2O
22mM S5a peptide U-15N,13C50mM sodium phosphate; 100mM sodium chloride; 5% D2O
Sample conditionsIonic strength: 150mM / pH: 6.5 / Pressure: ambient / Temperature: 300 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Bruker Karlsruheprocessing
AURELIA2.8.9Neidigdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 474 distance restraints, 452 are NOE-derived distance restraints, 22 are from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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://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