1XPA | pdb_00001xpa

SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN REPAIR FACTOR XPA, NMR, 1 STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1XPA/pdb
• BMRB: 4249

• Classification: DNA REPAIR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-07-06 Released: 1999-07-22 
• Deposition Author(s): Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K., Shirakawa, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 140 
• Conformers Submitted: 1 
• Selection Criteria: THE LOWEST ENERGY AND NO VIOLATION GREATER THAN 0.3A OR 5DEG 

Literature

Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA.

Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K., Shirakawa, M.

(1998) Nat Struct Biol 5: 701-706

• PubMed: 9699634 
• DOI: https://doi.org/10.1038/1400
• Primary Citation of Related Structures:  
  1XPA


• PubMed Abstract: 
  

  The solution structure of the central domain of the human nucleotide excision repair protein XPA, which binds to damaged DNA and replication protein A (RPA), was determined by nuclear magnetic resonance (NMR) spectroscopy. The central domain consists of a zinc-containing subdomain and a C-terminal subdomain. The zinc-containing subdomain has a compact globular structure and is distinct from the zinc-fingers found in transcription factors. The C-terminal subdomain folds into a novel alpha/beta structure with a positively charged superficial cleft. From the NMR spectra of the complexes, DNA and RPA binding surfaces are suggested.

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Organizational Affiliation: 

Graduate School of Biological Sciences, Nara Institute of Sciences and Technology, Ikoma, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.79 kDa 
• Atom Count: 944 
• Modelled Residue Count: 113 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XPA	A	122	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P23025 (Homo sapiens) Explore P23025  Go to UniProtKB:  P23025
PHAROS:  P23025 GTEx:  ENSG00000136936

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 140 
• Conformers Submitted: 1 
• Selection Criteria: THE LOWEST ENERGY AND NO VIOLATION GREATER THAN 0.3A OR 5DEG 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-22 
Deposition Author(s): Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K., Shirakawa, M.

Revision History  

• Version 1.0: 1999-07-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection