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- PDB-8s82: Restriction on Ku Inward Translocation Caps Telomere Ends -

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Basic information

Entry
Database: PDB / ID: 8s82
TitleRestriction on Ku Inward Translocation Caps Telomere Ends
Components
  • ATP-dependent DNA helicase II subunit 1
  • ATP-dependent DNA helicase II subunit 2
  • 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')
  • 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')
KeywordsDNA BINDING PROTEIN / Telomere / NHEJ / Rap1 / Ku / Chromosome / DNA Repair / Mutagenesis
Function / homology
Function and homology information


donor selection / mitochondrial double-strand break repair via homologous recombination / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / double-strand break repair via break-induced replication / telomerase RNA binding / recombinational repair / silent mating-type cassette heterochromatin formation / telomeric DNA binding ...donor selection / mitochondrial double-strand break repair via homologous recombination / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / double-strand break repair via break-induced replication / telomerase RNA binding / recombinational repair / silent mating-type cassette heterochromatin formation / telomeric DNA binding / subtelomeric heterochromatin formation / Neutrophil degranulation / telomere maintenance / DNA helicase activity / helicase activity / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / nuclear envelope / chromatin organization / DNA helicase / damaged DNA binding / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
: / Ku70 / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain ...: / Ku70 / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent DNA helicase II subunit 1 / ATP-dependent DNA helicase II subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsMattarocci, S. / Baconnais, S. / Roisne-Hamelin, F. / Pobiega, S. / Alibert, O. / Morin, V. / Deshayes, A. / Veaute, X. / Ropars, V. / Mazon, G. ...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 support France, 5items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM)EQU202203014702 France
Agence Nationale de la Recherche (ANR)ANR-15CE12-0007 DNA-Life France
Fondation ARC France
La ligue contre le cancer France
French Alternative Energies and Atomic Energy Commission (CEA) France
CitationJournal: Nat Commun / Year: 2025
Title: Restriction of Ku translocation protects telomere ends.
Authors: Stefano Mattarocci / Sonia Baconnais / Florian Roisné-Hamelin / Sabrina Pobiega / Olivier Alibert / Vincent Morin / Alice Deshayes / Xavier Veaute / Virginie Ropars / Maelenn Chevreuil / ...Authors: Stefano Mattarocci / Sonia Baconnais / Florian Roisné-Hamelin / Sabrina Pobiega / Olivier Alibert / Vincent Morin / Alice Deshayes / Xavier Veaute / Virginie Ropars / Maelenn Chevreuil / Johannes Mehringer / Didier Busso / Gerard Mazon / Paloma Fernandez Varela / Éric Le Cam / Jean-Baptiste Charbonnier / Philippe Cuniasse / Stéphane Marcand /
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 ...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.
History
DepositionMar 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: ATP-dependent DNA helicase II subunit 1
L: ATP-dependent DNA helicase II subunit 2
D: 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')
C: 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')


Theoretical massNumber of molelcules
Total (without water)154,9574
Polymers154,9574
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ATP-dependent DNA helicase II subunit 1


Mass: 70745.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: KU70_YEAST ATP-dependent DNA helicase II subunit 1 OS=Saccharomyces cerevisiae
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKU70 / Production host: Escherichia coli (E. coli) / References: UniProt: P32807
#2: Protein ATP-dependent DNA helicase II subunit 2


Mass: 71324.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: KU80_YEAST ATP-dependent DNA helicase II subunit 2
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKU80 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04437
#3: DNA chain 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')


Mass: 6643.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 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')


Mass: 6244.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast Ku, DNA Binary complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 10 mM Tris-HCl, 50 mM NaCl, pH 8.04
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: DNA 6 E-6 M Ku 6 E-6 M
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4cryoSPARC4CTF correction
7NAMD2.14model fittingMDFF protocole
9PHENIX1.21model refinementRealSpaceRefinement
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 689183 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingB value: 124.5 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
15Y58

5y58

K5Y58K1
25Y58

5y58

L5Y58L1
33UKG

3ukg

D3UKGD2
43UKG

3ukg

C3UKGC2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310410
ELECTRON MICROSCOPYf_angle_d0.5214239
ELECTRON MICROSCOPYf_dihedral_angle_d15.5314038
ELECTRON MICROSCOPYf_chiral_restr0.0411598
ELECTRON MICROSCOPYf_plane_restr0.0041683

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