Crystal structure of the redefined DNA-binding domain of human XPA

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Structural characterization of the redefined DNA-binding domain of human XPA.

Lian, F.M.Yang, X.Yang, W.Jiang, Y.L.Qian, C.

(2019) Biochem Biophys Res Commun 514: 985-990

  • DOI: https://doi.org/10.1016/j.bbrc.2019.05.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    XPA (xeroderma pigmentosum complementation group A), a key scaffold protein in nucleotide excision repair (NER) pathway, is important in DNA damage verification and repair proteins recruitment. Earlier studies had mapped the minimal DNA-binding domain (MBD) of XPA to a region corresponding to residues 98-219. However, recent studies indicated that the region involving residues 98-239 is the redefined DNA-binding domain (DBD), which binds to DNA substrates with a much higher binding affinity than MBD and possesses a nearly identical binding affinity to the full-length XPA protein. However, the structure of the redefined DBD domain of XPA (XPA-DBD) remains to be investigated. Here, we present the crystal structure of XPA-DBD at 2.06 Å resolution. Structure of the C-terminal region of XPA has been extended by 21 residues (Arg211-Arg231) as compared with previously reported MBD structures. The structure reveals that the C-terminal extension (Arg211-Arg231) is folded as an α-helix with multiple basic residues. The positively charged surface formed in the last C-terminal helix suggests its critical role in DNA binding. Further structural analysis demonstrates that the last C-terminal region (Asp217-Thr239) of XPA-DBD might undergo a conformational change to directly bind to the DNA substrates. This study provides a structural basis for understanding the possible mechanism of enhanced DNA-binding affinity of XPA-DBD.

  • Organizational Affiliation

    School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China. Electronic address: cmqian@hku.hk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein complementing XP-A cells145Homo sapiensMutation(s): 0 
Gene Names: XPAXPAC
UniProt & NIH Common Fund Data Resources
Find proteins for P23025 (Homo sapiens)
Explore P23025 
Go to UniProtKB:  P23025
GTEx:  ENSG00000136936 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23025
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.982α = 90
b = 66.982β = 90
c = 35.462γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31700672

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references