Crystal structure of an XPD DNA complex

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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Functional and Structural Studies of the Nucleotide Excision Repair Helicase Xpd Suggest a Polarity for DNA Translocation.

Kuper, J.Wolski, S.C.Michels, G.Kisker, C.

(2011) EMBO J 31: 494

  • DOI: https://doi.org/10.1038/emboj.2011.374
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The XPD protein is a vital subunit of the general transcription factor TFIIH which is not only involved in transcription but is also an essential component of the eukaryotic nucleotide excision DNA repair (NER) pathway. XPD is a superfamily-2 5'-3' helicase containing an iron-sulphur cluster. Its helicase activity is indispensable for NER and it plays a role in the damage verification process. Here, we report the first structure of XPD from Thermoplasma acidophilum (taXPD) in complex with a short DNA fragment, thus revealing the polarity of the translocated strand and providing insights into how the enzyme achieves its 5'-3' directionality. Accompanied by a detailed mutational and biochemical analysis of taXPD, we define the path of the translocated DNA strand through the protein and identify amino acids that are critical for protein function.

  • Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany. jochen.kuper@virchow.uni-wuerzburg.de


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-DEPENDENT DNA HELICASE TA0057620Thermoplasma acidophilumMutation(s): 0 
Find proteins for Q9HM14 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HM14 
Go to UniProtKB:  Q9HM14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HM14
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*DTP*AP*CP*GP)-3'B [auth E]4N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.06α = 90
b = 79.06β = 90
c = 175.69γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description