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- PDB-8vf5: CryoEM structure of Ku homodimer in complex with linear DNA -

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Basic information

Entry
Database: PDB / ID: 8vf5
TitleCryoEM structure of Ku homodimer in complex with linear DNA
Components
  • (DNA (40-MER)) x 2
  • Non-homologous end joining protein Ku
KeywordsDNA BINDING PROTEIN / NHEJ / DNA repair / Mycobacterium tuberculosis / DNA synapsis
Function / homology
Function and homology information


positive regulation of ligase activity / DNA helicase complex / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / DNA recombination / protein homodimerization activity
Similarity search - Function
Non-homologous end joining protein Ku, prokaryotic type / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Non-homologous end joining protein Ku
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBaral, J. / Rouiller, I. / Das, A.K.
Funding support Australia, India, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2000934 Australia
Science and Engineering Research Board (SERB)CRG/2020/002622 India
CitationJournal: To Be Published
Title: First cryoEM structure of bacterial Ku in complex with DNA
Authors: Baral, J. / Rouiller, I. / Das, A.K.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 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
A: Non-homologous end joining protein Ku
B: Non-homologous end joining protein Ku
G: DNA (40-MER)
H: DNA (40-MER)


Theoretical massNumber of molelcules
Total (without water)91,8524
Polymers91,8524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Non-homologous end joining protein Ku / Mt-Ku


Mass: 33609.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mku, Rv0937c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P9WKD9
#2: DNA chain DNA (40-MER)


Mass: 12239.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (40-MER)


Mass: 12391.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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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: Ku homodimer from M.tubeculosis in complex with linear DNA
Type: COMPLEX
Details: Protein: Ku homodimer was recombination purified DNA: Chemically Synthesized
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: 50mM HEPES, 150mM NaCl, 2mM TCEP
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)1
2150 mMSodium chloride1
32 mMTris(2-carboxyethyl)phosphine hydrochloride1
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4681

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Processing

EM software
IDNameCategoryDetails
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fittingRigid body fit
8PHENIXmodel fittingRigid body fit
10PHENIXmodel refinement
11Cootmodel refinement
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
CTF correctionDetails: Peformed in CryoSPARC Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5967886
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: OTHER / Num. of particles: 635411 / Algorithm: FOURIER SPACE
Details: Mean resolution of the map was 3.25 A, generated using ResMap Respective histogram and 2D slices can be provided on request.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingAccession code: AF-P9WKD9-F1 / Source name: AlphaFold / Type: in silico model

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