Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.54 kDa 
• Atom Count: 1100 
• Modelled Residue Count: 126 
• Deposited Residue Count: 145 
• Unique protein chains: 1

6J44

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

• PDB DOI: 10.2210/pdb6J44/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2019-05-29 
• Deposition Author(s): Lian, F.M., Yang, X., Yang, W., Jiang, Y.L., Qian, C.
• Funding Organization(s): National Natural Science Foundation of China

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

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

• PubMed: 31092331 
• DOI: 10.1016/j.bbrc.2019.05.050
• Primary Citation of Related Structures:  
  6J44


• 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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein complementing XP-A cells	A	145	Homo sapiens	Mutation(s): 0  Gene Names: XPA, XPAC
UniProt & NIH Common Fund Data Resources
Find proteins for P23025 (Homo sapiens) Explore P23025  Go to UniProtKB:  P23025
PHAROS:  P23025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 66.982	α = 90
b = 66.982	β = 90
c = 35.462	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-07 
• Released Date: 2019-05-29 
Deposition Author(s): Lian, F.M., Yang, X., Yang, W., Jiang, Y.L., Qian, C.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31700672

Revision History  

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