8S8P | pdb_00008s8p

Restriction on Ku Inward Translocation Caps Telomere Ends


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Restriction of Ku translocation protects telomere ends.

Mattarocci, S.Baconnais, S.Roisne-Hamelin, F.Pobiega, S.Alibert, O.Morin, V.Deshayes, A.Veaute, X.Ropars, V.Chevreuil, M.Mehringer, J.Busso, D.Mazon, G.Fernandez Varela, P.Le Cam, E.Charbonnier, J.B.Cuniasse, P.Marcand, S.

(2025) Nat Commun 16: 6824-6824

  • DOI: https://doi.org/10.1038/s41467-025-61864-1
  • Primary Citation of Related Structures:  
    8S82, 8S8P

  • PubMed Abstract: 

    Safeguarding chromosome ends against fusions via nonhomologous end joining (NHEJ) is essential for genome integrity. Paradoxically, the conserved NHEJ core factor Ku binds telomere ends. How it is prevented from promoting NHEJ remains unclear, as does the mechanism that allows Ku to coexist with telomere-protective DNA binding proteins, Rap1 in Saccharomyces cerevisiae. Here, we find that Rap1 directly inhibits Ku's NHEJ function at telomeres. A single Rap1 molecule near a double-stand break suppresses NHEJ without displacing Ku in cells. Furthermore, Rap1 and Ku form a complex on short DNA duplexes in vitro. Cryo-EM shows Rap1 blocks Ku's inward translocation on DNA - an essential step for NHEJ at DSBs. Nanopore sequencing of telomere fusions confirms this mechanism protects native telomere ends. These findings uncover a telomere protection mechanism where Rap1 restricts Ku's inward translocation. This switches Ku from a repair-promoting to a protective role preventing NHEJ at telomeres.


  • Organizational Affiliation
    • Université Paris-Saclay, Université Paris Cité, CEA, Inserm, Institut de biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France. stefano.mattarocci@inserm.fr.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase II subunit 1C [auth K]557Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YKU70HDF1NES24YMR284WYM8021.10
EC: 3.6.4.12
UniProt
Find proteins for P32807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32807 
Go to UniProtKB:  P32807
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UniProt GroupP32807
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase II subunit 2D [auth L]587Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YKU80HDF2YMR106CYM9718.05C
EC: 3.6.4.12
UniProt
Find proteins for Q04437 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04437 
Go to UniProtKB:  Q04437
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UniProt GroupQ04437
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding protein RAP1E [auth R]242Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAP1GRF1TUF1YNL216WN1310
UniProt
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11938 
Go to UniProtKB:  P11938
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UniProt GroupP11938
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*CP*AP*C)-3')A [auth C]21synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')B [auth D]21synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondation pour la Recherche Medicale (FRM)FranceEQU202203014702
Agence Nationale de la Recherche (ANR)FranceANR-15CE12-0007 DNA-Life
Fondation ARCFrance--
La ligue contre le cancerFrance--
French Alternative Energies and Atomic Energy Commission (CEA)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references