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

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Basic information

Entry
Database: PDB / ID: 8s8p
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')
  • DNA-binding protein RAP1
KeywordsDNA BINDING PROTEIN / Telomere / NHEJ / Rap1 / Ku / Chromosome / DNA Repair / Mutagenesis
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 / shelterin complex / telomere maintenance via telomere lengthening / 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 / DNA binding, bending / silent mating-type cassette heterochromatin formation / regulation of glycolytic process / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / TBP-class protein binding / Neutrophil degranulation / telomere maintenance / double-strand break repair via homologous recombination / protein-DNA complex / double-strand break repair via nonhomologous end joining / nuclear envelope / chromatin organization / DNA helicase / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / histone binding / damaged DNA binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / DNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single 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, 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: To Be Published
Title: A Restriction on Ku Inward Translocation Caps Telomere Ends
Authors: Mattarocci, S. / Baconnais, S. / Roisne-Hamelin, F. / Pobiega, S. / Alibert, O. / Morin, V. / Deshayes, A. / Le Cam, E. / Veaute, X. / Ropars, V. / Busso, D. / Mazon, G. / Fernandez Varela, ...Authors: Mattarocci, S. / Baconnais, S. / Roisne-Hamelin, F. / Pobiega, S. / Alibert, O. / Morin, V. / Deshayes, A. / Le Cam, E. / Veaute, X. / Ropars, V. / Busso, D. / Mazon, G. / Fernandez Varela, P. / Charbonnier, J.B. / Cuniasse, P. / Marcand, S.
History
DepositionMar 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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')
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')
K: ATP-dependent DNA helicase II subunit 1
L: ATP-dependent DNA helicase II subunit 2
R: DNA-binding protein RAP1


Theoretical massNumber of molelcules
Total (without water)173,2575
Polymers173,2575
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30450 Å2
ΔGint-178 kcal/mol
Surface area75810 Å2
MethodPISA

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Components

#1: 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)
#2: 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)
#3: Protein ATP-dependent DNA helicase II subunit 1 / ATP-dependent DNA helicase II subunit Ku70 / High affinity DNA-binding factor subunit 1


Mass: 65531.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKU70, HDF1, NES24, YMR284W, YM8021.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P32807, DNA helicase
#4: Protein ATP-dependent DNA helicase II subunit 2 / ATP-dependent DNA helicase II subunit Ku80 / High affinity DNA-binding factor subunit 2 / Yeast Ku80


Mass: 66469.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKU80, HDF2, YMR106C, YM9718.05C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04437, DNA helicase
#5: Protein DNA-binding protein RAP1 / Repressor/activator site-binding protein / SBF-E / TUF


Mass: 28368.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAP1, GRF1, TUF1, YNL216W, N1310 / Production host: Escherichia coli (E. coli) / References: UniProt: P11938
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

Component
IDNameTypeEntity IDParent-IDSource
1Ternary Complex of Ku Rap1 and DNACOMPLEX#3-#4, #2, #1, #50MULTIPLE SOURCES
2ATP-dependent DNA helicase II and DNA-binding protein RAP1COMPLEX#3-#51RECOMBINANT
3Double stranded DNACOMPLEX#2, #11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (brewer's yeast)4932
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
Buffer solutionpH: 8 / Details: Tris-HCL 10mM, Nacl 50 mM, pH 8.04
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 750 nm / Nominal defocus min: 250 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4particle selection
7NAMD2.14model fittingMDFF protocole
9PHENIX1.21model refinementRealSpaceRefinement of the final MDF model
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1544386
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 436644 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial 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.
Atomic model buildingDetails: Model build using PDB entries 5Y58 and 3UKG / Source name: Other / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212465
ELECTRON MICROSCOPYf_angle_d0.52317018
ELECTRON MICROSCOPYf_dihedral_angle_d16.4451938
ELECTRON MICROSCOPYf_chiral_restr0.0391884
ELECTRON MICROSCOPYf_plane_restr0.0042055

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