[English] 日本語
Yorodumi
- PDB-2kde: NMR structure of major S5a (196-306):K48 linked diubiquitin species -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kde
TitleNMR structure of major S5a (196-306):K48 linked diubiquitin species
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • Ubiquitin
KeywordsPROTEIN BINDING / protein complex / ubiquitin interacting motifs / Cytoplasm / Nucleus / Ubl conjugation / Alternative splicing / Phosphoprotein / Proteasome
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 / cytoplasm
Similarity search - Function
Helix Hairpins - #3990 / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Helix Hairpins - #3990 / : / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Helix Hairpins / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4 / Polyubiquitin
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhang, N. / Wang, Q. / Ehlinger, A. / Randles, L. / Lary, J.W. / Kang, Y. / Haririnia, A. / Cole, J.L. / Fushman, D. / Walters, K.J.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.
Authors: Zhang, N. / Wang, Q. / Ehlinger, A. / Randles, L. / Lary, J.W. / Kang, Y. / Haririnia, A. / Storaska, A.J. / Cole, J.L. / Fushman, D. / Walters, K.J.
History
DepositionJan 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 4
B: Ubiquitin
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)28,9813
Polymers28,9813
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)7 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein 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 / ASF / AF


Mass: 11826.878 Da / Num. of mol.: 1 / Fragment: UNP residues 196-306, S5a fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55036
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62972
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
2223D 1H-13C NOESY
2333D 13C-filtered 1H-13C NOESY
2443D 13C-filtered 1H-13C NOESY
2553D 13C-filtered 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N; U-50% 2H] S5a (196-306)-1, 1.2 mM K48 linked diubiquitin-2, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C] S5a (196-306)-3, 1.5 mM K48 linked diubiquitin-4, 100% D2O100% D2O
30.5 mM [U-100% 13C of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-5, 1.0 mM S5a (196-306)-6, 100% D2O100% D2O
40.5 mM [U-100% 13C of the distal subunit; natural abundance of the proximal Ub] K48 linked diubiquitin-7, 1.0 mM S5a (196-306)-8, 100% D2O100% D2O
50.4 mM [U-100% 13C] S5a (196-306)-9, 1.2 mM [U-100% 2H of the proximal Ub; natural abundance of the distal subunit] ] K48 linked diubiquitin-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMS5a (196-306)-1[U-100% 15N; U-50% 2H]1
1.2 mMK48 linked diubiquitin-21
0.5 mMS5a (196-306)-3[U-100% 13C]2
1.5 mMK48 linked diubiquitin-42
0.5 mMK48 linked diubiquitin-5[U-100% 13C of the proximal Ub; natural abundance of the distal subunit]3
1.0 mMS5a (196-306)-63
0.5 mMK48 linked diubiquitin-7[U-100% 13C of the distal subunit; natural abundance of the proximal Ub]4
1.0 mMS5a (196-306)-84
0.4 mMS5a (196-306)-9[U-100% 13C]5
1.2 mMK48 linked diubiquitin-10[U-100% 2H of the proximal Ub; natural abundance of the distal subunit] ]5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM NaPO4; 100 mM NaCl 6.5ambient 298 K
220 mM NaPO4; 50 mM NaCl 6.5ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

-
Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.data analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 7

+
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