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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 / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / nuclear envelope / chromatin organization / DNA helicase / 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 / 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 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 ...: / 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 / 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: 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 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

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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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