2WYQ

THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.651 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of the Ubiquitin-Like (Ubl) Domain of Human Homologue a of Rad23 (Hhr23A) Protein

Chen, Y.W.Tajima, T.Agrawal, S.

(2011) Protein Eng.Des.Sel. 24: 131

  • DOI: 10.1093/protein/gzq084

  • PubMed Abstract: 
  • The human homologue of the yeast Rad23 protein, hHR23A, plays dual roles in DNA repair as well as in translocating polyubiquitinated proteins to the proteasome. We determined the three-dimensional structure of its ubiquitin-like (UbL) domain by X-ray ...

    The human homologue of the yeast Rad23 protein, hHR23A, plays dual roles in DNA repair as well as in translocating polyubiquitinated proteins to the proteasome. We determined the three-dimensional structure of its ubiquitin-like (UbL) domain by X-ray crystallography. It has the same overall structure and fold characteristics as ubiquitin and other members of the UbL domain family, with overall root mean square deviations in Cα positions in the range of 1.0-1.3 Å. There are local differences in the α1-β3 loop where hHR23A UbL domain has three more residues constituting a bigger loop. Analysis of the crystal packing revealed a possible dimeric arrangement mediated by the three residues (Leu10, Ile49 and Met75) that are known to be critical for molecular interactions. In contrast to the overall well-defined structure, these three residues are either disordered or have multiple conformations, suggesting that conformation variability is an important property of the binding surface. The electrostatic potentials at the binding surface are conserved among the family, with the hHR23B domain being the most similar to this structure. The intra-molecular complexes formed by the UbL domain of hHR23A with its UbA1 or UbA2 domains was studied by comparative homology modelling, which suggests these two interactions are structurally similar and are mutually exclusive.


    Related Citations: 
    • DNA-Repair Protein Hhr23A Alters its Protein Structure Upon Binding Proteasomal Subunit S5A.
      Walters, K.J.,Lech, P.J.,Goh, A.M.,Wang, Q.,Howley, P.M.
      (2003) Proc.Natl.Acad.Sci.USA 100: 12694
    • Crystallization and Preliminary X-Ray Diffraction Studies of the Ubiquitin-Like (Ubl) Domain of the Human Homologue a of Rad23 (Hhr23A) Protein.
      Chen, Y.W.,Tajima, T.,Rees, M.,Garcia-Maya, M.
      (2009) Acta Crystallogr.,Sect.F 65: 930
    • Structural Determinants for the Binding of Ubiquitin-Like Domains to the Proteasome.
      Mueller, T.D.,Feigon, J.
      (2003) Embo J. 22: 4634


    Organizational Affiliation

    King's College London, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, London SE11UL, UK. yu-wai.chen@kcl.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
A
85Homo sapiensMutation(s): 0 
Gene Names: RAD23A
Find proteins for P54725 (Homo sapiens)
Go to Gene View: RAD23A
Go to UniProtKB:  P54725
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.651 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.124 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.434α = 90.00
b = 78.434β = 90.00
c = 63.472γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-11-19 
  • Released Date: 2010-11-10 
  • Deposition Author(s): Chen, Y.W.

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance