5XRZ

Structure of a ssDNA bound to the inner DNA binding site of RAD52

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural Basis of Homology-Directed DNA Repair Mediated by RAD52

Saotome, M., Saito, K., Yasuda, T., Ohtomo, H., Sugiyama, S., Nishimura, Y., Kurumizaka, H., Kagawa, W.

(2018) iScience 3: 50-62

  • DOI: 10.1016/j.isci.2018.04.005
  • Primary Citation of Related Structures:  
    5XRZ, 5XS0

  • PubMed Abstract: 

    • RAD52 mediates homologous recombination by annealing cDNA strands. However, the detailed mechanism of DNA annealing promoted by RAD52 has remained elusive. Here we report two crystal structures of human RAD52 single-stranded DNA (ssDNA) complexes that probably represent key reaction intermediates of RAD52-mediated DNA annealing ...

    RAD52 mediates homologous recombination by annealing cDNA strands. However, the detailed mechanism of DNA annealing promoted by RAD52 has remained elusive. Here we report two crystal structures of human RAD52 single-stranded DNA (ssDNA) complexes that probably represent key reaction intermediates of RAD52-mediated DNA annealing. The first structure revealed a "wrapped" conformation of ssDNA around the homo-oligomeric RAD52 ring, in which the edges of the bases involved in base pairing are exposed to the solvent. The ssDNA conformation is close to B-form and appears capable of engaging in Watson-Crick base pairing with the cDNA strand. The second structure revealed a "trapped" conformation of ssDNA between two RAD52 rings. This conformation is stabilized by a different RAD52 DNA binding site, which promotes the accumulation of multiple RAD52 rings on ssDNA and the aggregation of ssDNA. These structures provide a structural framework for understanding the mechanism of RAD52-mediated DNA annealing.

    Organizational Affiliation: 

    Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan. Electronic address: wataru.kagawa@meisei-u.ac.jp.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein RAD52 homolog
A, B, C, D, E, F, G, H, I, J, K
A, B, C, D, E, F, G, H, I, J, K
215Homo sapiensMutation(s): 2 
Gene Names: RAD52
UniProt & NIH Common Fund Data Resources
Find proteins for P43351 (Homo sapiens)
Explore P43351 
Go to UniProtKB:  P43351
PHAROS:  P43351
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43351
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
ssDNA (40-MER)L40synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.621α = 91.89
b = 101.42β = 108.68
c = 101.71γ = 108.17
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JSPS KAKENHIJapanJP24570138
JSPS KAKENHIJapanJP26116521
JSPS KAKENHIJapanJP16H01316
Japan Private School Promotion FoundationJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references