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- EMDB-19790: Restriction on Ku Inward Translocation Caps Telomere Ends -

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Basic information

Entry
Database: EMDB / ID: EMD-19790
TitleRestriction on Ku Inward Translocation Caps Telomere Ends
Map dataFull map
Sample
  • Complex: Yeast Ku, DNA Binary complex
    • Protein or peptide: ATP-dependent DNA helicase II subunit 1
    • Protein or peptide: ATP-dependent DNA helicase II subunit 2
    • DNA: 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')
    • DNA: 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')
KeywordsTelomere / NHEJ / Rap1 / Ku / Chromosome / DNA Repair / Mutagenesis / DNA BINDING PROTEIN
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
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)
Methodsingle 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, 5 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19790.png

Downloads & links

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Map

FileDownload / File: emd_19790.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 336.384 Å		0.66 Å/pix.
x 512 pix.
= 336.384 Å		0.66 Å/pix.
x 512 pix.
= 336.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.657 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.091
Minimum - Maximum-1.3771838 - 1.866667
Average (Standard dev.)-0.0001973952 (±0.02092467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 336.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_19790_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19790_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast Ku, DNA Binary complex

EntireName: Yeast Ku, DNA Binary complex
Components
  • Complex: Yeast Ku, DNA Binary complex
    • Protein or peptide: ATP-dependent DNA helicase II subunit 1
    • Protein or peptide: ATP-dependent DNA helicase II subunit 2
    • DNA: 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')
    • DNA: 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')

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Supramolecule #1: Yeast Ku, DNA Binary complex

SupramoleculeName: Yeast Ku, DNA Binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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

MacromoleculeName: ATP-dependent DNA helicase II subunit 1 / type: protein_or_peptide / ID: 1
Details: KU70_YEAST ATP-dependent DNA helicase II subunit 1 OS=Saccharomyces cerevisiae
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 70.74532 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRSVTNAFGN SGELNDQVDE TGYRKFDIHE GILFCIELSE TMFKESSDLE YKSPLLEILE SLDELMSQLV ITRPGTAIGC YFYYCNRED AKEGIYELFP LRDINATFMK KLNDLLEDLS SGRISLYDYF MFQQTGSEKQ VRLSVLFTFM LDTFLEEIPG Q KQLSNKRV ...String:
MRSVTNAFGN SGELNDQVDE TGYRKFDIHE GILFCIELSE TMFKESSDLE YKSPLLEILE SLDELMSQLV ITRPGTAIGC YFYYCNRED AKEGIYELFP LRDINATFMK KLNDLLEDLS SGRISLYDYF MFQQTGSEKQ VRLSVLFTFM LDTFLEEIPG Q KQLSNKRV FLFTDIDKPQ EAQDIDERAR LRRLTIDLFD NKVNFATFFI GYADKPFDNE FYSDILQLGS HTNENTGLDS EF DGPSTKP IDAKYIKSRI LRKKEVKRIM FQCPLILDEK TNFIVGVKGY TMYTHEKAGV RYKLVYEHED IRQEAYSKRK FLN PITGED VTGKTVKVYP YGDLDINLSD SQDQIVMEAY TQKDAFLKII GFRSSSKSIH YFNNIDKSSF IVPDEAKYEG SIRT LASLL KILRKKDKIA ILWGKLKSNS HPSLYTLSPS SVKDYNEGFY LYRVPFLDEI RKFPSLLSYD DGSEHKLDYD NMKKV TQSI MGYFNLRDGY NPSDFKNPLL QKHYKVLHDY LLQIETTFDE NETPNTKKDR MMREDDSLRK LYYIRNKILE SEKSED PII QRLNKYVKIW NMFYKKFNDD NISIKEEKKP FDKKPKFNI

UniProtKB: ATP-dependent DNA helicase II subunit 1

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Macromolecule #2: ATP-dependent DNA helicase II subunit 2

MacromoleculeName: ATP-dependent DNA helicase II subunit 2 / type: protein_or_peptide / ID: 2 / Details: KU80_YEAST ATP-dependent DNA helicase II subunit 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 71.324844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSESTTFIV DVSPSMMKNN NVSKSMAYLE YTLLNKSKKS RKTDWISCYL ANCPVSENSQ EIPNVFQIQS FLAPVTTTAT IGFIKRLKQ YCDQHSHDSS NEGLQSMIQC LLVVSLDIKQ QFQARKILKQ IVVFTDNLDD LDITDEEIDL LTEELSTRII L IDCGKDTQ ...String:
MSSESTTFIV DVSPSMMKNN NVSKSMAYLE YTLLNKSKKS RKTDWISCYL ANCPVSENSQ EIPNVFQIQS FLAPVTTTAT IGFIKRLKQ YCDQHSHDSS NEGLQSMIQC LLVVSLDIKQ QFQARKILKQ IVVFTDNLDD LDITDEEIDL LTEELSTRII L IDCGKDTQ EERKKSNWLK LVEAIPNSRI YNMNELLVEI TSPATSVVKP VRVFSGELRL GADILSTQTS NPSGSMQDEN CL CIKVEAF PATKAVSGLN RKTAVEVEDS QKKERYVGVK SIIEYEIHNE GNKKNVSEDD QSGSSYIPVT ISKDSVTKAY RYG ADYVVL PSVLVDQTVY ESFPGLDLRG FLNREALPRY FLTSESSFIT ADTRLGCQSD LMAFSALVDV MLENRKIAVA RYVS KKDSE VNMCALCPVL IEHSNINSEK KFVKSLTLCR LPFAEDERVT DFPKLLDRTT TSGVPLKKET DGHQIDELME QFVDS MDTD ELPEIPLGNY YQPIGEVTTD TTLPLPSLNK DQEENKKDPL RIPTVFVYRQ QQVLLEWIHQ LMINDSREFE IPELPD SLK NKISPYTHKK FDSTKLVEVL GIKKVDKLKL DSELKTELER EKIPDLETLL KRGEQHSRGS PNNSNN

UniProtKB: ATP-dependent DNA helicase II subunit 2

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Macromolecule #3: DNA (5'-D(*GP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*TP*GP*...

MacromoleculeName: 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')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.643248 KDa
SequenceString:
(DG)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DG) (DG)(DG)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DG) (DT)

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Macromolecule #4: DNA (5'-D(*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*...

MacromoleculeName: 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')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.244084 KDa
SequenceString:
(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC) (DC)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DC)(DA) (DC)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 10 mM Tris-HCl, 50 mM NaCl, pH 8.04
VitrificationCryogen name: ETHANE
DetailsDNA 6 E-6 M Ku 6 E-6 M

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 689183
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5y58

chain_id: K, source_name: PDB, initial_model_type: experimental model

5y58

chain_id: L, source_name: PDB, initial_model_type: experimental model

3ukg

chain_id: D, source_name: PDB, initial_model_type: experimental model

3ukg

chain_id: C, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 124.5
Output model

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

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