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- EMDB-39800: cryo-EM map of RNF168(1-193) in complex with Ubc5c-Ub conjugated ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39800
Titlecryo-EM map of RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosome at a resolution of 3.23 angstrom
Map data3.23 angstrom cryo-EM map of RNF168(1-193)-Ubc5c-NCP complex
Sample
  • Complex: RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosomes
Keywordsnucleosome / RNF168 / H2AK13/15 / UbcH5c-Ub / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsAi HS / Tong ZB / Deng ZH / Tian CL / Liu L / Pan M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168.
Authors: Huasong Ai / Zebin Tong / Zhiheng Deng / Qiang Shi / Shixian Tao / Gaoge Sun / Jiawei Liang / Maoshen Sun / Xiangwei Wu / Qingyun Zheng / Lujun Liang / Hang Yin / Jia-Bin Li / Shuai Gao / ...Authors: Huasong Ai / Zebin Tong / Zhiheng Deng / Qiang Shi / Shixian Tao / Gaoge Sun / Jiawei Liang / Maoshen Sun / Xiangwei Wu / Qingyun Zheng / Lujun Liang / Hang Yin / Jia-Bin Li / Shuai Gao / Changlin Tian / Lei Liu / Man Pan /
Abstract: The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent ...The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent K13 and K15 (K13/15) sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to site-specifically ubiquitinate H2A K13/15 has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c~Ub (ubiquitin) in complex with nucleosomes. Here we developed chemical strategies and determined the cryo-electron microscopy structures of the RNF168-UbcH5c~Ub-nucleosome complex captured in transient H2A K13/15 monoubiquitination and adjacent dual monoubiquitination reactions, providing a 'helix-anchoring' mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the 'compass-binding' mode of dimeric E3 ligases. Our work not only provides structural snapshots of H2A K13/15 site-specific monoubiquitination and adjacent dual monoubiquitination but also offers a near-atomic-resolution structural framework for understanding pathogenic amino acid substitutions and physiological modifications of RNF168.
History
DepositionApr 19, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39800.png

Downloads & links

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Map

FileDownload / File: emd_39800.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.23 angstrom cryo-EM map of RNF168(1-193)-Ubc5c-NCP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 222.643 Å		0.87 Å/pix.
x 256 pix.
= 222.643 Å		0.87 Å/pix.
x 256 pix.
= 222.643 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.012658969 - 0.03501457
Average (Standard dev.)0.00024639812 (±0.0016500234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.6432 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 4.54 angstrom cryo-EM map of RNF168(1-193)-Ubc5c complex

Fileemd_39800_additional_1.map
Annotation4.54 angstrom cryo-EM map of RNF168(1-193)-Ubc5c complex
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: 3.59 angstrom cryo-EM map of RNF168(1-193)-Ubc5c-Ub-NCP complex

Fileemd_39800_additional_2.map
Annotation3.59 angstrom cryo-EM map of RNF168(1-193)-Ubc5c-Ub-NCP complex
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_39800_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39800_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosomes

EntireName: RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosomes
Components
  • Complex: RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosomes

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Supramolecule #1: RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosomes

SupramoleculeName: RNF168(1-193) in complex with Ubc5c-Ub conjugated nucleosomes
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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.066 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81043
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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