4ERN

Crystal structure of the C-terminal domain of human XPB/ERCC-3 excision repair protein at 1.80 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE.

Hilario, E.Li, Y.Nobumori, Y.Liu, X.Fan, L.

(2013) Acta Crystallogr.,Sect.D 69: 237-246

  • DOI: 10.1107/S0907444912045040

  • PubMed Abstract: 
  • XPB is a DNA-dependent helicase and a subunit of the TFIIH complex required for both transcription and DNA repair. XPB contains four domains: an N-terminal domain, two conserved helicase domains (HD1 and HD2) and a C-terminal extension. The C-termina ...

    XPB is a DNA-dependent helicase and a subunit of the TFIIH complex required for both transcription and DNA repair. XPB contains four domains: an N-terminal domain, two conserved helicase domains (HD1 and HD2) and a C-terminal extension. The C-terminal extension is important for DNA repair since the phosphorylation of Ser751 inhibits 5'-incision by ERCC1-XPF endonuclease. A disease-causing frameshift mutation (XP11BE) that changes the last 42 amino acids of XPB causes manifestations including impaired DNA repair and deficient transcription. Here, the crystal structure of the C-terminal half of XPB (residues 494-782) is reported at 1.8 Å resolution. The structure contained the conserved XPB HD2 and a C-terminal extension which shares structural similarity with RIG-I, leading to a structural model of the XPF-XPB-DNA complex for 5' incision during DNA repair. A mutation mimicking the XP11BE mutation produced the much less soluble mutant XPBm(494-781). Western blotting results confirmed that the intracellular levels of XPB and other TFIIH subunits in XP11BE patient cells were much lower than those from the healthy parents. Together, these results indicate that the XP11BE mutation not only divests the XPF-interaction motif, impairing DNA repair, but also reduces XPB solubility, leading to a lower intracellular level of TFIIH and deficient transcription.


    Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TFIIH basal transcription factor complex helicase XPB subunit
A
289Homo sapiensGene Names: ERCC3 (XPB, XPBC)
EC: 3.6.4.12
Find proteins for P19447 (Homo sapiens)
Go to Gene View: ERCC3
Go to UniProtKB:  P19447
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.260α = 90.00
b = 73.650β = 90.00
c = 84.300γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CrystalCleardata collection
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXrefinement
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence