1KN0

Crystal Structure of the human Rad52 protein

• PDB DOI: https://doi.org/10.2210/pdb1KN0/pdb

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


• Deposited: 2001-12-18 Released: 2002-09-04 
• Deposition Author(s): Kagawa, W., Kurumizaka, H., Ishitani, R., Fukai, S., Nureki, O., Shibata, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.297 
• R-Value Work: 0.231 
• R-Value Observed: 0.236 

Literature

Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form.

Kagawa, W., Kurumizaka, H., Ishitani, R., Fukai, S., Nureki, O., Shibata, T., Yokoyama, S.

(2002) Mol Cell 10: 359-371

• PubMed: 12191481 
• DOI: https://doi.org/10.1016/s1097-2765(02)00587-7
• Primary Citation of Related Structures:  
  1KN0


• PubMed Abstract: 
  

  The human Rad52 protein forms a heptameric ring that catalyzes homologous pairing. The N-terminal half of Rad52 is the catalytic domain for homologous pairing, and the ring formed by the domain fragment was reported to be approximately decameric. Splicing variants of Rad52 and a yeast homolog (Rad59) are composed mostly of this domain. In this study, we determined the crystal structure of the homologous-pairing domain of human Rad52 and revealed that the domain forms an undecameric ring. Each monomer has a beta-beta-beta-alpha fold, which consists of highly conserved amino acid residues among Rad52 homologs. A mutational analysis revealed that the amino acid residues located between the beta-beta-beta-alpha fold and the characteristic hairpin loop are essential for ssDNA and dsDNA binding.

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Organizational Affiliation: 

RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C11  (Explore in 3D)
Global Stoichiometry: Homo 11-mer - A11 

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

Macromolecule Content

• Total Structure Weight: 257.75 kDa 
• Atom Count: 16,032 
• Modelled Residue Count: 2,024 
• Deposited Residue Count: 2,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rad52	A, B, C, D, E, F, G, H, I, J, K	212	Homo sapiens	Mutation(s): 0  Gene Names: Rad52
UniProt & NIH Common Fund Data Resources
Find proteins for P43351 (Homo sapiens) Explore P43351  Go to UniProtKB:  P43351
PHAROS:  P43351 GTEx:  ENSG00000002016

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.297 
• R-Value Work: 0.231 
• R-Value Observed: 0.236 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.61	α = 90
b = 145.61	β = 90
c = 247.53	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-04 
Deposition Author(s): Kagawa, W., Kurumizaka, H., Ishitani, R., Fukai, S., Nureki, O., Shibata, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2002-09-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references