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- EMDB-70949: Distal Ku-Polymerase lambda BRCT -

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Basic information

Entry
Database: EMDB / ID: EMD-70949
TitleDistal Ku-Polymerase lambda BRCT
Map data
Sample
  • Complex: NHEJ Short-range complex with Polymerase lambda
    • Complex: DNA ligase 4, DNA repair protein XRCC4
    • Complex: Polymerase lambda, Non-homologous end-joining factor 1, Protein PAXX
KeywordsDNA repair / NHEJ / Complex / Polymerase / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsVogt A / He Y
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144559 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 United States
CitationJournal: To Be Published
Title: End Processing in NHEJ by Polymerase lambda and PNKP is coordinated during short-range synapsis
Authors: Vogt A / Kaminski AM / Pedersen LC / Naila T / Tomkinson AE / Lees-Miller SP / Kunkel TA / He Y
History
DepositionJun 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70949.png

Downloads & links

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Map

FileDownload / File: emd_70949.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 416 pix.
= 439.296 Å		1.06 Å/pix.
x 416 pix.
= 439.296 Å		1.06 Å/pix.
x 416 pix.
= 439.296 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-2.5700696 - 3.8952727
Average (Standard dev.)-0.0005480862 (±0.009921963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 439.296 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70949_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_70949_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 : NHEJ Short-range complex with Polymerase lambda

EntireName: NHEJ Short-range complex with Polymerase lambda
Components
  • Complex: NHEJ Short-range complex with Polymerase lambda
    • Complex: DNA ligase 4, DNA repair protein XRCC4
    • Complex: Polymerase lambda, Non-homologous end-joining factor 1, Protein PAXX

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Supramolecule #1: NHEJ Short-range complex with Polymerase lambda

SupramoleculeName: NHEJ Short-range complex with Polymerase lambda / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: DNA ligase 4, DNA repair protein XRCC4

SupramoleculeName: DNA ligase 4, DNA repair protein XRCC4 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Polymerase lambda, Non-homologous end-joining factor 1, Protein PAXX

SupramoleculeName: Polymerase lambda, Non-homologous end-joining factor 1, Protein PAXX
type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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: 7.9
Component:
ConcentrationFormulaName
50.0 mMKClPotassium Chloride
10.0 mMHEPES
5.0 percentglycerol
1.0 mMDTT
0.01 percentNP-40
5.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSample stabilized by GraFix

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.61 sec. / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1506486
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lsy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 179057
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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