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- EMDB-52849: Apo-MtbKu , not bound to DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-52849
TitleApo-MtbKu , not bound to DNA
Map data
Sample
  • Complex: Apo-MtbKu
    • Protein or peptide: Non-homologous end joining protein Ku
KeywordsDNA repair / tuberculosis / NHEJ / DNA BINDING PROTEIN
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
Non-homologous end joining protein Ku
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.41 Å
AuthorsChaplin AK / Zahid S
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/X00029X/1 United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
CitationJournal: To Be Published
Title: Apo-MtbKu , not bound to DNA
Authors: Chaplin AK / Zahid S
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52849.png

Downloads & links

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Map

FileDownload / File: emd_52849.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0789
Minimum - Maximum-0.11076996 - 0.29575586
Average (Standard dev.)0.001381467 (±0.010055957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52849_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52849_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo-MtbKu

EntireName: Apo-MtbKu
Components
  • Complex: Apo-MtbKu
    • Protein or peptide: Non-homologous end joining protein Ku

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Supramolecule #1: Apo-MtbKu

SupramoleculeName: Apo-MtbKu / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: Non-homologous end joining protein Ku

MacromoleculeName: Non-homologous end joining protein Ku / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.47757 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHVG TGSNDDDDKS PDPMRAIWTG SIAFGLVNVP VKVYSATADH DIRFHQVHAK DNGRIRYKRV CEACGEVVDY RDLARAYES GDGQMVAITD DDIASLPEER SREIEVLEFV PAADVDPMMF DRSYFLEPDS KSSKSYVLLA KTLAETDRMA I VHFTLRNK ...String:
MAHHHHHHVG TGSNDDDDKS PDPMRAIWTG SIAFGLVNVP VKVYSATADH DIRFHQVHAK DNGRIRYKRV CEACGEVVDY RDLARAYES GDGQMVAITD DDIASLPEER SREIEVLEFV PAADVDPMMF DRSYFLEPDS KSSKSYVLLA KTLAETDRMA I VHFTLRNK TRLAALRVKD FGKREVMMVH TLLWPDEIRD PDFPVLDQKV EIKPAELKMA GQVVDSMADD FNPDRYHDTY QE QLQELID TKLEGGQAFT AEDQPRLLDE PEDVSDLLAK LEASVKARSK ANSNVPTPP

UniProtKB: Non-homologous end joining protein Ku

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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
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
75.0 mMNaClSodium Chloride
5.0 mMMgCl2Magnesium Chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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