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- EMDB-4762: Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB -

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Basic information

Entry
Database: EMDB / ID: EMD-4762
TitleCryo-EM structure of NCP-6-4PP(-1)-UV-DDB
Map data
SampleUV-DDB bound to a 6-4PP containing nucleosome:
(histonesHistone) x 2 / DNA damage-binding proteins / DNA / Histone H3.1Histone H3 / (Histone H4) x 2 / Histone H2A type 1-B/E / Histone H2B type 1-J / (nucleic-acidNucleic acid) x 2 / (DNA damage-binding protein ...) x 2
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / : / Cul4B-RING E3 ubiquitin ligase complex / UV-damage excision repair / histone H2A monoubiquitination / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / biological process involved in interaction with symbiont / Cul4-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / : / Cul4B-RING E3 ubiquitin ligase complex / UV-damage excision repair / histone H2A monoubiquitination / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / biological process involved in interaction with symbiont / Cul4-RING E3 ubiquitin ligase complex / cullin family protein binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / positive regulation of gluconeogenesis / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Chromatin modifying enzymes / Deposition of new CENPA-containing nucleosomes at the centromere / proteasomal protein catabolic process / DNA replication-independent chromatin assembly / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / protein autoubiquitination / Meiotic synapsis / positive regulation of viral genome replication / heterochromatin assembly => GO:0031507 / pyrimidine dimer repair / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Interleukin-7 signaling / DNA replication-dependent chromatin assembly / response to UV / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / Defective pyroptosis / : / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nucleotide-excision repair / nuclear chromosome / Recognition of DNA damage by PCNA-containing replication complex / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Metalloprotease DUBs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Dual Incision in GG-NER / DNA Damage/Telomere Stress Induced Senescence / lipopolysaccharide binding / G2/M DNA damage checkpoint / nucleosome assembly / RMTs methylate histone arginines / positive regulation of protein catabolic process / HCMV Early Events / Formation of Incision Complex in GG-NER / HDMs demethylate histones / Pre-NOTCH Transcription and Translation / Dual incision in TC-NER / Meiotic recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / regulation of circadian rhythm / PKMTs methylate histone lysines / nucleosome / protein-macromolecule adaptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Wnt signaling pathway / UCH proteinases / Transcriptional regulation of granulopoiesis / protein polyubiquitination / Neddylation / rhythmic process / site of double-strand break / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / proteasome-mediated ubiquitin-dependent protein catabolic process / cell junction / ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromosome, telomeric region / killing of cells of another organism
Similarity search - Function
DNA damage-binding protein 2 / DNA damage-binding protein 1 / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. ...DNA damage-binding protein 2 / DNA damage-binding protein 1 / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats 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 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMatsumoto S / Cavadini S / Bunker RD / Thoma NH
Funding support Switzerland, Japan, 7 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII3_160734/1 Switzerland
European Commission667951
European Union666068
Japan Society for the Promotion of ScienceJP18H05534 Japan
European Commission705354
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of ScienceJP16H06307 Japan
CitationJournal: Nature / Year: 2019
Title: DNA damage detection in nucleosomes involves DNA register shifting.
Authors: Syota Matsumoto / Simone Cavadini / Richard D Bunker / Ralph S Grand / Alessandro Potenza / Julius Rabl / Junpei Yamamoto / Andreas D Schenk / Dirk Schübeler / Shigenori Iwai / Kaoru ...Authors: Syota Matsumoto / Simone Cavadini / Richard D Bunker / Ralph S Grand / Alessandro Potenza / Julius Rabl / Junpei Yamamoto / Andreas D Schenk / Dirk Schübeler / Shigenori Iwai / Kaoru Sugasawa / Hitoshi Kurumizaka / Nicolas H Thomä /
Abstract: Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced ...Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer or a DNA-damage mimic in various positions. We find that UV-DDB binds UV-damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA.
History
DepositionApr 2, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseJun 12, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r8y
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4762.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.)
0.86 Å/pix.
x 300 pix.
= 258. Å
0.86 Å/pix.
x 300 pix.
= 258. Å
0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-14.282898 - 32.150463
Average (Standard dev.)0.00045621197 (±0.9515588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-14.28332.1500.000

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Supplemental data

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Sample components

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Entire UV-DDB bound to a 6-4PP containing nucleosome

EntireName: UV-DDB bound to a 6-4PP containing nucleosome / Number of Components: 14

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Component #1: protein, UV-DDB bound to a 6-4PP containing nucleosome

ProteinName: UV-DDB bound to a 6-4PP containing nucleosome / Recombinant expression: No
MassTheoretical: 199 kDa

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Component #2: protein, histones

ProteinName: histonesHistone / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, DNA damage-binding proteins

ProteinName: DNA damage-binding proteins / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: synthetic construct (others)

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Component #5: protein, histones

ProteinName: histonesHistone / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H3.1

ProteinName: Histone H3.1Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.719445 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #7: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.676703 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.447825 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #9: protein, Histone H2B type 1-J

ProteinName: Histone H2B type 1-J / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.217516 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #10: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: nucleic-acid, Human alpha-satellite DNA (145-MER)

nucleic acidName: Human alpha-satellite DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)(DA) (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)
MassTheoretical: 44.780672 kDa
SourceSpecies: Homo sapiens (human)

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Component #12: nucleic-acid, Human alpha-satellite DNA (145-MER) with a 6-4PP at...

nucleic acidName: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96
Class: DNA
Details: 145 bp human alpha-satellite with a 6-4 pyrimidine-pyrimidone (6-4PP) at base positions 95-96
Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)(T64)(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)
MassTheoretical: 44.709645 kDa
SourceSpecies: Homo sapiens (human)

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Component #13: protein, DNA damage-binding protein 1

ProteinName: DNA damage-binding protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 127.425812 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #14: protein, DNA damage-binding protein 2

ProteinName: DNA damage-binding protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.261277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.4
VitrificationInstrument: LEICA EM GP / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 85 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: SPOT SCAN
LensMagnification: 130000.0 X (nominal) / Cs: 0 mm / Imaging Mode: BRIGHT FIELD / Energy Filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 84000
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target Criteria: Cross-correlation coefficient / Refinement space: REAL
Input PDB model: 4ZUX, 4ZUX, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 4E54, 3EI4
Chain ID: I, J, A, B, C, D, E, F, G, H, B, A
Output model

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