[English] 日本語
Yorodumi
- PDB-1dv0: Refined NMR solution structure of the C-terminal UBA domain of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dv0
TitleRefined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)
ComponentsDNA REPAIR PROTEIN HHR23A
KeywordsDNA BINDING PROTEIN / Helical bundle
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair ...regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair / DNA Damage Recognition in GG-NER / protein destabilization / kinase binding / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / 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-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated 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-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsWithers-Ward, E.S. / Mueller, T.D. / Chen, I.S. / Feigon, J.
Citation
Journal: Biochemistry / Year: 2000
Title: Biochemical and structural analysis of the interaction between the UBA(2) domain of the DNA repair protein HHR23A and HIV-1 Vpr
Authors: Withers-Ward, E.S. / Mueller, T.D. / Chen, I.S. / Feigon, J.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of a Human DNA Repair Protein UBA Domain that Interacts with HIV-1 Vpr
Authors: Dieckmann, T. / Withers-Ward, E.S. / Jarosinski, M.A. / Liu, C.F. / Chen, I.S. / Feigon, J.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 11, 2000ID: 1UBA
Revision 1.0Feb 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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: DNA REPAIR PROTEIN HHR23A


Theoretical massNumber of molelcules
Total (without water)5,2961
Polymers5,2961
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)18 / 100structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #6closest to the average

-
Components

#1: Protein/peptide DNA REPAIR PROTEIN HHR23A


Mass: 5295.841 Da / Num. of mol.: 1 / Fragment: UBA DOMAIN (C-TERMINAL DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T (PHARMACIA) / Production host: Escherichia coli (E. coli) / References: UniProt: P54725

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141DQF-COSY
NMR detailsText: This structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM Uba-domain, chemically synthesized; 50mM potassium phosphate pH 6.5; 90% H2O, 10% D2O90% H2O/10% D2O
22mM Uba-domain, expressed in E.coli, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O95% H2O/5% D2O
32mM Uba-domain, U-15N, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O95% H2O/5% D2O
42mM Uba-domain, U-15N,13C, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 50mM sodium phosphate, 100mM sodium chloride
pH: 6.5 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukerprocessing
XEASY1.3.10Bartels, Xia, Billeter, Guntert, Wuthrichdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 796 restraints, 779 are NOE-derived, 17 distance restraints are from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

+
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