8S8P | pdb_00008s8p

Restriction on Ku Inward Translocation Caps Telomere Ends

PDB DOI: https://doi.org/10.2210/pdb8S8P/pdb
EM Map EMD-19811: EMDB EMDataResource
NAKB: 8S8P

Classification: DNA BINDING PROTEIN
Organism(s): synthetic construct, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-07 Released: 2025-06-18
Deposition Author(s): Mattarocci, S., Baconnais, S., Roisne-Hamelin, F., Pobiega, S., Alibert, O., Morin, V., Deshayes, A., Veaute, X., Ropars, V., Mazon, G., Busso, D., Fernandez Varela, P., Le Cam, E., Charbonnier, J., Cuniasse, P., Marcand, S.
Funding Organization(s): Fondation pour la Recherche Medicale (FRM), Agence Nationale de la Recherche (ANR), Fondation ARC, La ligue contre le cancer, French Alternative Energies and Atomic Energy Commission (CEA)

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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wwPDB Validation 3D Report Full Report

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

PubMed: 40707444 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-61864-1
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 173.26 kDa
Atom Count: 12,134
Modeled Residue Count: 1,428
Deposited Residue Count: 1,428
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase II subunit 1	C [auth K]	557	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: YKU70, HDF1, NES24, YMR284W, YM8021.10 EC: 3.6.4.12
UniProt
Find proteins for P32807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32807 Go to UniProtKB: P32807
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32807
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase II subunit 2	D [auth L]	587	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: YKU80, HDF2, YMR106C, YM9718.05C EC: 3.6.4.12
UniProt
Find proteins for Q04437 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04437 Go to UniProtKB: Q04437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04437
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein RAP1	E [auth R]	242	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RAP1, GRF1, TUF1, YNL216W, N1310
UniProt
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11938 Go to UniProtKB: P11938
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11938
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(APCPAPCPAPCPAPCPAPCPCPCPAPCPAPCPAPCPCPAP*C)-3')	A [auth C]	21	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(GPTPGPGPTPGPTPGPTPGPGPGPTPGPTPGPTPGPTPGP*T)-3')	B [auth D]	21	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21
RECONSTRUCTION	cryoSPARC	4.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Fondation pour la Recherche Medicale (FRM)	France	EQU202203014702
Agence Nationale de la Recherche (ANR)	France	ANR-15CE12-0007 DNA-Life
Fondation ARC	France	--
La ligue contre le cancer	France	--
French Alternative Energies and Atomic Energy Commission (CEA)	France	--