8BJM | pdb_00008bjm

Human full length RAD52 undecamer.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An integrative structural study of the human full-length RAD52 at 2.2 angstrom resolution.

Balboni, B.Marotta, R.Rinaldi, F.Milordini, G.Varignani, G.Girotto, S.Cavalli, A.

(2024) Commun Biol 7: 956-956

  • DOI: https://doi.org/10.1038/s42003-024-06644-1
  • Primary Citation of Related Structures:  
    8BJM

  • PubMed Abstract: 

    Human RAD52 (RAD52) is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel pharmacological target for anticancer strategies. Although the interest in RAD52 has exponentially grown in the previous decade, most information about its structure and mechanism still needs to be elucidated. Here, we report the 2.2 Å resolution cryo-EM reconstruction of the full-length RAD52 (FL-RAD52) protein. This allows us to describe the hydration shell of the N-terminal region of FL-RAD52, which is structured in an undecamer ring. Water molecules coordinate with protein residues to promote stabilization inside and among the protomers and within the inner DNA binding cleft to drive protein-DNA recognition. Additionally, through a multidisciplinary approach involving SEC-SAXS and computational methods, we comprehensively describe the highly flexible and dynamic organization of the C-terminal portion of FL-RAD52. This work discloses unprecedented structural details on the FL-RAD52, which will be critical for characterizing its mechanism of action and inhibitor development, particularly in the context of novel approaches to synthetic lethality and anticancer drug discovery.


  • Organizational Affiliation
    • Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD52 homolog
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K
432Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43351
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
iNEXT-DiscoveryEuropean Union15983
Italian Association for Cancer ResearchItalyIG 2018 Id.21386

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Structure summary
  • Version 1.2: 2024-05-29
    Changes: Database references
  • Version 1.3: 2024-08-14
    Changes: Data collection, Database references