6LAE

Crystal structure of the DNA-binding domain of human XPA in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


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Literature

New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA.

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

(2020) Int.J.Biol.Macromol. 148: 466-474

  • DOI: 10.1016/j.ijbiomac.2020.01.169

  • PubMed Abstract: 
  • XPA (Xeroderma pigmentosum complementation group A) is a core scaffold protein that plays significant roles in DNA damage verification and recruiting downstream endonucleases in the nucleotide excision repair (NER) pathway. Here, we present the 2.81  ...

    XPA (Xeroderma pigmentosum complementation group A) is a core scaffold protein that plays significant roles in DNA damage verification and recruiting downstream endonucleases in the nucleotide excision repair (NER) pathway. Here, we present the 2.81 Å resolution crystal structure of the DNA-binding domain (DBD) of human XPA in complex with an undamaged splayed-arm DNA substrate with a single pair of non-complementary nucleotides. The structure reveals that two XPA molecules bind to one splayed-arm DNA with a 10-bp duplex recognition motif in a non-sequence-specific manner. XPA molecules bind to both ends of the DNA duplex region with a characteristic β-hairpin. A conserved tryptophan residue Trp175 packs against the last base pair of DNA duplex and stabilizes the conformation of the characteristic β-hairpin. Upon DNA binding, the C-terminal last helix of XPA would shift towards the minor groove of the DNA substrate for better interaction. Notably, human XPA is able to bind to the undamaged DNA duplex without any kinks, and XPA-DNA binding does not bend the DNA substrate obviously. This study provides structural basis for the binding mechanism of XPA to the undamaged splayed-arm DNA with a single pair of non-complementary nucleotides.


    Organizational Affiliation

    School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China. Electronic address: cmqian@hku.hk.,Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,Institute of Behavioral Medicine Education of Shandong Province, Jining Medical University, Jining, Shandong 272067, China; Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, China.,Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, China. Electronic address: fmlian@mail.jnmc.edu.cn.,Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, China.,Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, China; Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair protein complementing XP-A cells
A, B
145Homo sapiensMutation(s): 0 
Gene Names: XPA (XPAC)
Find proteins for P23025 (Homo sapiens)
Go to Gene View: XPA
Go to UniProtKB:  P23025
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3')C11Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3')D11Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 69.112α = 90.00
b = 69.112β = 90.00
c = 63.938γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31700672

Revision History 

  • Version 1.0: 2020-02-26
    Type: Initial release