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- EMDB-61247: Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-61247
TitleCryo-EM structure of UV-DDB bound to native NCP at SHL+/-3
Map data
Sample
  • Complex: Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3
KeywordsDNA repair / Nucleosome / UV-DDB / DNA damage / DDB2 / NER / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMatsumoto S / Takizawa Y / Ogasawara M / Hashimoto K / Negishi L / Xu W / Tachibana H / Yamamoto J / Iwai S / Sugasawa K / Kurumizaka H
Funding support Japan, 11 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K18034 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02319 Japan
Japan Science and TechnologyJPMJPR2288 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome.
Authors: Syota Matsumoto / Yoshimasa Takizawa / Mitsuo Ogasawara / Kana Hashimoto / Lumi Negishi / Wenjie Xu / Haruna Tachibana / Junpei Yamamoto / Shigenori Iwai / Kaoru Sugasawa / Hitoshi Kurumizaka /
Abstract: In mammalian global genomic nucleotide excision repair, UV-DDB plays a central role in recognizing DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers, within chromatin. In the ...In mammalian global genomic nucleotide excision repair, UV-DDB plays a central role in recognizing DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers, within chromatin. In the present study, we perform cryo-electron microscopy analyses coupled with chromatin-immunoprecipitation to reveal that the cellular UV-DDB binds to UV-damaged DNA lesions in a chromatin unit, the nucleosome, at a position approximately 20 base-pairs from the nucleosomal dyad in human cells. An alternative analysis of the in vitro reconstituted UV-DDB-cyclobutane pyrimidine dimer nucleosome structure demonstrates that the DDB2 subunit of UV-DDB specifically recognizes the cyclobutane pyrimidine dimer lesion at this position on the nucleosome. We also determine the structures of UV-DDB bound to DNA lesions at other positions in purified cellular human nucleosomes. These cellular and reconstituted UV-DDB-nucleosome complex structures provide important evidence for understanding the mechanism by which UV lesions in chromatin are recognized and repaired in mammalian cells.
History
DepositionAug 21, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61247.png

Downloads & links

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Map

FileDownload / File: emd_61247.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.008043478 - 0.027097005
Average (Standard dev.)0.000051181472 (±0.00066998904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61247_half_map_1.map
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Half map: #2

Fileemd_61247_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3

EntireName: Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3
Components
  • Complex: Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3

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Supramolecule #1: Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3

SupramoleculeName: Cryo-EM structure of UV-DDB bound to native NCP at SHL+/-3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 10.0 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9220
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6
FSC plot (resolution estimation)

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