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- EMDB-61243: Cryo-EM structure of NCP-UV-DDB complex containing CPD -

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Entry
Database: EMDB / ID: EMD-61243
TitleCryo-EM structure of NCP-UV-DDB complex containing CPD
Map dataCPD
Sample
  • Complex: Cryo-EM structure of NCP-UV-DDB complex containing CPD
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: Human alpha-satellite DNA (145-MER)
    • DNA: Human alpha-satellite DNA (145-MER) with CPD at position 95
    • Protein or peptide: DNA damage-binding protein 2
KeywordsDNA repair / Nucleosome / UV-DDB / DNA damage / DDB2 / NER / DNA BINDING PROTEIN
Function / homology
Function and homology information


UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / site of DNA damage / pyrimidine dimer repair / negative regulation of tumor necrosis factor-mediated signaling pathway / response to UV / negative regulation of megakaryocyte differentiation / protein autoubiquitination ...UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / site of DNA damage / pyrimidine dimer repair / negative regulation of tumor necrosis factor-mediated signaling pathway / response to UV / negative regulation of megakaryocyte differentiation / protein autoubiquitination / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / epigenetic regulation of gene expression / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / DNA Damage Recognition in GG-NER / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Dual Incision in GG-NER / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / protein polyubiquitination / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to UV / structural constituent of chromatin / UCH proteinases / cell junction / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / killing of cells of another organism / gene expression / Estrogen-dependent gene expression / damaged DNA binding / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA repair
Similarity search - Function
DNA damage-binding protein 2 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A ...DNA damage-binding protein 2 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 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_61243.png

Downloads & links

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Map

FileDownload / File: emd_61243.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCPD
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.020856325 - 2.210803
Average (Standard dev.)0.0008870475 (±0.020598253)
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: #2

Fileemd_61243_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61243_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of NCP-UV-DDB complex containing CPD

EntireName: Cryo-EM structure of NCP-UV-DDB complex containing CPD
Components
  • Complex: Cryo-EM structure of NCP-UV-DDB complex containing CPD
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: Human alpha-satellite DNA (145-MER)
    • DNA: Human alpha-satellite DNA (145-MER) with CPD at position 95
    • Protein or peptide: DNA damage-binding protein 2

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Supramolecule #1: Cryo-EM structure of NCP-UV-DDB complex containing CPD

SupramoleculeName: Cryo-EM structure of NCP-UV-DDB complex containing CPD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: DNA damage-binding protein 2

MacromoleculeName: DNA damage-binding protein 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.93293 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP QILPPCRSIV RTLHQHKLGR ASWPSVQQG LQQSFLHTLD SYRILQKAAP FDRRATSLAW HPTHPSTVAV GSKGGDIMLW NFGIKDKPTF IKGIGAGGSI T GLKFNPLN ...String:
MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP QILPPCRSIV RTLHQHKLGR ASWPSVQQG LQQSFLHTLD SYRILQKAAP FDRRATSLAW HPTHPSTVAV GSKGGDIMLW NFGIKDKPTF IKGIGAGGSI T GLKFNPLN TNQFYASSME GTTRLQDFKG NILRVFASSD TINIWFCSLD VSASSRMVVT GDNVGNVILL NMDGKELWNL RM HKKKVTH VALNPCCDWF LATASVDQTV KIWDLRQVRG KASFLYSLPH RHPVNAACFS PDGARLLTTD QKSEIRVYSA SQW DCPLGL IPHPHRHFQH LTPIKAAWHP RYNLIVVGRY PDPNFKSCTP YELRTIDVFD GNSGKMMCQL YDPESSGISS LNEF NPMGD TLASAMGYHI LIWSQEEART RK

UniProtKB: DNA damage-binding protein 2

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Macromolecule #5: Human alpha-satellite DNA (145-MER)

MacromoleculeName: Human alpha-satellite DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.756648 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DT)(DT)(DC)(DA)(DG) (DC)(DT)(DG) (DA)(DA)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG) (DG)(DA)(DG)(DC) (DA)(DG)(DT)(DT)(DT) (DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC) (DT)(DT)(DT)(DT)(DG) (DG)(DT)(DA)(DG) (DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DT)(DG)(DG)(DA)(DT)(DA) (DT)(DT)(DG) (DA)(DT)

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Macromolecule #6: Human alpha-satellite DNA (145-MER) with CPD at position 95

MacromoleculeName: Human alpha-satellite DNA (145-MER) with CPD at position 95
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.709645 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DT)(DG)(DA)(DA)(DC)(DC)(DA)(DG) (DC)(DT)(DG) (DA)(DA)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(TTD)(DG) (DA)(DG)(DC) (DA)(DG)(DT)(DT)(DT)(DC) (DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC)(DT) (DT)(DT)(DT)(DG) (DG)(DT)(DA)(DG)(DA) (DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG)(DT) (DG)(DG)(DA)(DT)(DA) (DT)(DT)(DG)(DA) (DT)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.53 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: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6
FSC plot (resolution estimation)

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