8RD4 | pdb_00008rd4

Telomeric RAP1:DNA-PK complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 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

Chromosome end protection by RAP1-mediated inhibition of DNA-PK.

Eickhoff, P.Sonmez, C.Fisher, C.E.L.Inian, O.Roumeliotis, T.I.Dello Stritto, A.Mansfeld, J.Choudhary, J.S.Guettler, S.Lottersberger, F.Douglas, M.E.

(2025) Nature 642: 1090-1096

  • DOI: https://doi.org/10.1038/s41586-025-08896-1
  • Primary Citation of Related Structures:  
    8RD4

  • PubMed Abstract: 

    During classical non-homologous end joining (cNHEJ), DNA-dependent protein kinase (DNA-PK) encapsulates free DNA ends, forming a recruitment platform for downstream end-joining factors including ligase 4 (LIG4) 1 . DNA-PK can also bind telomeres and regulate their resection 2-4 , but does not initiate cNHEJ at this position. How the end-joining process is regulated in this context-specific manner is currently unclear. Here we show that the shelterin components TRF2 and RAP1 form a complex with DNA-PK that directly represses its end-joining function at telomeres. Biochemical experiments and cryo-electron microscopy reveal that when bound to TRF2, RAP1 establishes a network of interactions with KU and DNA that prevents DNA-PK from recruiting LIG4. In mouse and human cells, RAP1 is redundant with the Apollo nuclease in repressing cNHEJ at chromosome ends, demonstrating that the inhibition of DNA-PK prevents telomere fusions in parallel with overhang-dependent mechanisms. Our experiments show that the end-joining function of DNA-PK is directly and specifically repressed at telomeres, establishing a molecular mechanism for how individual linear chromosomes are maintained in mammalian cells.


  • Organizational Affiliation
    • Telomere Biology Laboratory, The Institute of Cancer Research, London, UK.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78527 (Homo sapiens)
Explore P78527 
Go to UniProtKB:  P78527
PHAROS:  P78527
GTEx:  ENSG00000253729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78527
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Telomeric repeat-binding factor 2-interacting protein 1B [auth D]399Homo sapiensMutation(s): 0 
Gene Names: TERF2IP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYB0 (Homo sapiens)
Explore Q9NYB0 
Go to UniProtKB:  Q9NYB0
PHAROS:  Q9NYB0
GTEx:  ENSG00000166848 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYB0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6C [auth E]609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens)
Explore P12956 
Go to UniProtKB:  P12956
PHAROS:  P12956
GTEx:  ENSG00000196419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12956
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5D [auth F]732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens)
Explore P13010 
Go to UniProtKB:  P13010
PHAROS:  P13010
GTEx:  ENSG00000079246 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13010
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (41-MER)E [auth X]100synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (41-MER)F [auth Y]100synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC68409/A28129

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-16
    Changes: Data collection, Database references