[English] 日本語
Yorodumi
- PDB-1p9d: High-resolution structure of the complex of HHR23A ubiquitin-like... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p9d
TitleHigh-resolution structure of the complex of HHR23A ubiquitin-like domain and the C-terminal ubiquitin-interacting motif of proteasome subunit S5a
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • UV excision repair protein RAD23 homolog A
KeywordsREPLICATION / protein-peptide complex
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of cell cycle ...regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of cell cycle / positive regulation of viral genome replication / proteasome complex / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / nucleotide-excision repair / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / G2/M Checkpoints / protein destabilization / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / DNA Damage Recognition in GG-NER / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / kinase binding / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / molecular adaptor activity / Ub-specific processing proteases / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin interaction motif / UBA/TS-N domain ...RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin interaction motif / UBA/TS-N domain / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin associated domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / von Willebrand factor A-like domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog A / 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
S: 26S proteasome non-ATPase regulatory subunit 4
U: UV excision repair protein RAD23 homolog A


Theoretical massNumber of molelcules
Total (without water)13,8702
Polymers13,8702
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 / 30structures 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, PUBS2
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
#2: Protein UV excision repair protein RAD23 homolog A / HHR23A


Mass: 8953.532 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Production host: Escherichia coli (E. coli) / References: UniProt: P54725

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
12115N-,13C-filtered/edited 2D-NOESY
13215N-,13C-filtered/edited 2D-NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM S5a peptide unlabeled, 2mM ubiquitin-like domain of HHR23A U-15N,13C50mM sodium phosphate, 100mM sodium chloride, 5% D2O
22mM S5a peptide U-15N,13C, 2mM ubiquitin-like domain of HHR23A unlabeled50mM 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 2066 restraints, 1999 are NOE-derived distance restraints, of which 58 are intermolecular. For the S5a ubiquitin-interacting motif only the residues ...Details: The structures are based on a total of 2066 restraints, 1999 are NOE-derived distance restraints, of which 58 are intermolecular. For the S5a ubiquitin-interacting motif only the residues 270 to 301 were included in the structure calculations due to disorder of the flexible N- and C-termini.
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://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