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- EMDB-38102: Cryo-EM map of RNF168/UbcH5c-Ub/nucleosome determined by E2-Ub-NC... -

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Basic information

Entry
Database: EMDB / ID: EMD-38102
TitleCryo-EM map of RNF168/UbcH5c-Ub/nucleosome determined by E2-Ub-NCP conjugation strategy
Map data
Sample
  • Complex: RNF168/UbcH5c-Ub/nucleosome complex determined by E2-Ub-NCP conjugation strategy
KeywordsRNF168 / nucleosome / H2AK13/15 ubiquitination / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsAi H / Zebin T / Deng Z / Pan M / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, 22277073 China
CitationJournal: Biorxiv / Year: 2024
Title: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168
Authors: Ai H / Tong Z / Deng Z / Shi Q / Tao S / Liang J / Sun M / Wu X / Zheng Q / Liang L / Li JB / Gao S / Tian C / Liu L / Pan M
History
DepositionNov 24, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38102.png

Downloads & links

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Map

FileDownload / File: emd_38102.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.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.00306354 - 0.0166585
Average (Standard dev.)0.00030553725 (±0.0013517985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38102_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38102_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_38102_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 : RNF168/UbcH5c-Ub/nucleosome complex determined by E2-Ub-NCP conju...

EntireName: RNF168/UbcH5c-Ub/nucleosome complex determined by E2-Ub-NCP conjugation strategy
Components
  • Complex: RNF168/UbcH5c-Ub/nucleosome complex determined by E2-Ub-NCP conjugation strategy

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Supramolecule #1: RNF168/UbcH5c-Ub/nucleosome complex determined by E2-Ub-NCP conju...

SupramoleculeName: RNF168/UbcH5c-Ub/nucleosome complex determined by E2-Ub-NCP conjugation strategy
type: complex / ID: 1 / Parent: 0
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.0 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: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10209
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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