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- EMDB-75074: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75074
TitleNucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1, Consensus map
Map data
Sample
  • Complex: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
KeywordsDNA damage binding protein / DNA BINDING PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKim TH / Jayathilake C / Virk RK / Gregory-Lott ER
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154859 United States
American Cancer SocietyIRG-16-186-21 United States
CitationJournal: To Be Published
Title: High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks
Authors: Jayathilake C / Mewhinney CE / Virk RK / Gregory-Lott ER / Nair R / Yang J / Cho E / Day AG / Taylor DJ / Kim TH
History
DepositionJan 12, 2026-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75074.png

Downloads & links

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Map

FileDownload / File: emd_75074.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.051
Minimum - Maximum-0.1735344 - 0.377502
Average (Standard dev.)0.0009165661 (±0.013793653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75074_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_75074_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 : Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain...

EntireName: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
Components
  • Complex: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2

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Supramolecule #1: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain...

SupramoleculeName: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 29.55 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 50551
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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