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- EMDB-19811: Restriction on Ku Inward Translocation Caps Telomere Ends -

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Basic information

Entry
Database: EMDB / ID: EMD-19811
TitleRestriction on Ku Inward Translocation Caps Telomere Ends
Map datafull map
Sample
  • Complex: Ternary Complex of Ku Rap1 and DNA
    • Complex: ATP-dependent DNA helicase II and DNA-binding protein RAP1
      • Protein or peptide: ATP-dependent DNA helicase II subunit 1
      • Protein or peptide: ATP-dependent DNA helicase II subunit 2
      • Protein or peptide: DNA-binding protein RAP1
    • Complex: Double stranded DNA
      • 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


positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / donor selection / mitochondrial double-strand break repair via homologous recombination / telomeric G-quadruplex DNA binding / protein localization to chromosome / protection from non-homologous end joining at telomere / establishment of protein-containing complex localization to telomere / establishment of protein localization to telomere / Ku70:Ku80 complex ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / donor selection / mitochondrial double-strand break repair via homologous recombination / telomeric G-quadruplex DNA binding / protein localization to chromosome / protection from non-homologous end joining at telomere / establishment of protein-containing complex localization to telomere / establishment of protein localization to telomere / Ku70:Ku80 complex / telomere maintenance via telomere lengthening / shelterin complex / establishment of protein localization to chromatin / double-stranded telomeric DNA binding / G-quadruplex DNA binding / double-strand break repair via break-induced replication / telomerase RNA binding / recombinational repair / silent mating-type cassette heterochromatin formation / regulation of glycolytic process / DNA binding, bending / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / Neutrophil degranulation / telomere maintenance / DNA helicase activity / TBP-class protein binding / double-strand break repair via homologous recombination / helicase activity / protein-DNA complex / double-strand break repair via nonhomologous end joining / nuclear envelope / chromatin organization / histone binding / transcription regulator complex / damaged DNA binding / DNA helicase / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
Rap1, DNA-binding domain / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / : / Ku70 / Ku80 / Ku70/Ku80 C-terminal arm ...Rap1, DNA-binding domain / Rap1, DNA-binding / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / : / Ku70 / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta 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 / BRCT domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / breast cancer carboxy-terminal domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA-binding protein RAP1 / 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: 3.11 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 7, 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_19811.png

Downloads & links

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Map

FileDownload / File: emd_19811.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)

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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-0.9283182 - 1.2578673
Average (Standard dev.)-0.00014810369 (±0.017917851)
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_19811_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_19811_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary Complex of Ku Rap1 and DNA

EntireName: Ternary Complex of Ku Rap1 and DNA
Components
  • Complex: Ternary Complex of Ku Rap1 and DNA
    • Complex: ATP-dependent DNA helicase II and DNA-binding protein RAP1
      • Protein or peptide: ATP-dependent DNA helicase II subunit 1
      • Protein or peptide: ATP-dependent DNA helicase II subunit 2
      • Protein or peptide: DNA-binding protein RAP1
    • Complex: Double stranded DNA
      • 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: Ternary Complex of Ku Rap1 and DNA

SupramoleculeName: Ternary Complex of Ku Rap1 and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4, #2, #1, #5

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Supramolecule #2: ATP-dependent DNA helicase II and DNA-binding protein RAP1

SupramoleculeName: ATP-dependent DNA helicase II and DNA-binding protein RAP1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Double stranded DNA

SupramoleculeName: Double stranded DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #1
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: 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: 1 / 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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Macromolecule #2: 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: 2 / 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 #3: ATP-dependent DNA helicase II subunit 1

MacromoleculeName: ATP-dependent DNA helicase II subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 65.531449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IHEGILFCIE LSETMFKESS DLEYKSPLLE ILESLDELMS QLVITRPGTA IGCYFYYCNR EDAKEGIYEL FPLRDINATF MKKLNDLLE DLSSGRISLY DYFMFQQTGS EKQVRLSVLF TFMLDTFLEE IPGQKQLSNK RVFLFTDIDK PQEAQDIDER A RLRRLTID ...String:
IHEGILFCIE LSETMFKESS DLEYKSPLLE ILESLDELMS QLVITRPGTA IGCYFYYCNR EDAKEGIYEL FPLRDINATF MKKLNDLLE DLSSGRISLY DYFMFQQTGS EKQVRLSVLF TFMLDTFLEE IPGQKQLSNK RVFLFTDIDK PQEAQDIDER A RLRRLTID LFDNKVNFAT FFIGYADKPF DNEFYSDILQ LGSHTNENTG LDSEFDGPST KPIDAKYIKS RILRKKEVKR IM FQCPLIL DEKTNFIVGV KGYTMYTHEK AGVRYKLVYE HEDIRQEAYS KRKFLNPITG EDVTGKTVKV YPYGDLDINL SDS QDQIVM EAYTQKDAFL KIIGFRSSSK SIHYFNNIDK SSFIVPDEAK YEGSIRTLAS LLKILRKKDK IAILWGKLKS NSHP SLYTL SPSSVKDYNE GFYLYRVPFL DEIRKFPSLL SYDDGSEHKL DYDNMKKVTQ SIMGYFNLRD GYNPSDFKNP LLQKH YKVL HDYLLQIETT FDENETPNTK KDRMMREDDS LRKLYYIRNK ILESEKSEDP IIQRLNKYVK IWNMFYKKFN DDN

UniProtKB: ATP-dependent DNA helicase II subunit 1

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Macromolecule #4: ATP-dependent DNA helicase II subunit 2

MacromoleculeName: ATP-dependent DNA helicase II subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 66.469398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SSESTTFIVD VSPSMMKNNN VSKSMAYLEY TLLNKSKKSR KTDWISCYLA NCPVSENSQE IPNVFQIQSF LAPVTTTATI GFIKRLKQY CDQHSHDSSN EGLQSMIQCL LVVSLDIKQQ FQARKILKQI VVFTDNLDDL DITDEEIDLL TEELSTRIIL I DCGKDTQE ...String:
SSESTTFIVD VSPSMMKNNN VSKSMAYLEY TLLNKSKKSR KTDWISCYLA NCPVSENSQE IPNVFQIQSF LAPVTTTATI GFIKRLKQY CDQHSHDSSN EGLQSMIQCL LVVSLDIKQQ FQARKILKQI VVFTDNLDDL DITDEEIDLL TEELSTRIIL I DCGKDTQE ERKKSNWLKL VEAIPNSRIY NMNELLVEIT SPATSVVKPV RVFSGELRLG ADILSTQTSN PSGSMQDENC LC IKVEAFP ATKAVSGLNR KTAVEVEDSQ KKERYVGVKS IIEYEIHNEG NKKNVSEDDQ SGSSYIPVTI SKDSVTKAYR YGA DYVVLP SVLVDQTVYE SFPGLDLRGF LNREALPRYF LTSESSFITA DTRLGCQSDL MAFSALVDVM LENRKIAVAR YVSK KDSEV NMCALCPVLI EHSNINSEKK FVKSLTLCRL PFAEDERVTD FPKLLDRTTT SGVPLKKETD GHQIDELMEQ FVDSM DTDE LPEIPLGNYY QPIGEVTTDT TLPLPSLNKD QEENKKDPLR IPTVFVYRQQ QVLLEWIHQL MINDSREFEI PELPDS LKN KISPYTHKKF DSTKLVEVLG IKKV

UniProtKB: ATP-dependent DNA helicase II subunit 2

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Macromolecule #5: DNA-binding protein RAP1

MacromoleculeName: DNA-binding protein RAP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.368781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KASFTDEEDE FILDVVRKNP TRRTTHTLYD EISHYVPNHT GNSIRHRFRV YLSKRLEYVY EVDKFGKLVR DDDGNLIKTK VLPPSIKRK FSADEDYTLA IAVKKQFYRD LFQIDPDTGR SLITDEDTPT AIARRNMTMD PNHVPGSEPN FAAYRTQSRR G PIAREFFK ...String:
KASFTDEEDE FILDVVRKNP TRRTTHTLYD EISHYVPNHT GNSIRHRFRV YLSKRLEYVY EVDKFGKLVR DDDGNLIKTK VLPPSIKRK FSADEDYTLA IAVKKQFYRD LFQIDPDTGR SLITDEDTPT AIARRNMTMD PNHVPGSEPN FAAYRTQSRR G PIAREFFK HFAEEHAAHT ENAWRDRFRK FLLAYGIDDY ISYYEAEKAQ NREPEPMKNL TNRPKRPGVP TPGNYNSAAK RA RN

UniProtKB: DNA-binding protein RAP1

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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: Tris-HCL 10mM, Nacl 50 mM, pH 8.04
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 0.75 µm / Nominal defocus min: 0.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1544386
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: The model was designed using a combination of PDB structures for KU (5Y58), DNA and RAP1 (3UKG)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 436644
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model build using PDB entries 5Y58 and 3UKG
DetailsInitial Fitting of the model in the cryo-EM map was achieved using ChimeraX and this structure served as starting point for MDFF refinement (Flexible fitting) using NAMD 2.14.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8s8p:
Restriction on Ku Inward Translocation Caps Telomere Ends

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