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- EMDB-4764: Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A -

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Basic information

Entry
Database: EMDB / ID: EMD-4764
TitleCryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Map data
SampleUV-DDB bound to a THF2 containing nucleosome class A
  • Histone H3.1, Histone H2A, Histone H2BHistone H3
  • (Histone H4) x 2
  • DNA
  • (DNA damage-binding protein ...) x 3
  • Histone H3.1Histone H3
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • (nucleic-acidNucleic acid) 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 / positive regulation of viral release from host cell / Cul4A-RING E3 ubiquitin ligase complex / UV-damage excision repair / histone H2A monoubiquitination / WD40-repeat domain binding / cullin-RING ubiquitin ligase complex / 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 / positive regulation of viral release from host cell / Cul4A-RING E3 ubiquitin ligase complex / UV-damage excision repair / histone H2A monoubiquitination / WD40-repeat domain binding / cullin-RING ubiquitin ligase complex / interaction with symbiont / Cul4-RING E3 ubiquitin ligase complex / cullin family protein binding / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / negative regulation of megakaryocyte differentiation / positive regulation of gluconeogenesis / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / telomere capping / positive regulation of viral genome replication / interleukin-7-mediated signaling pathway / chromatin silencing / regulation of mitotic cell cycle phase transition / protein autoubiquitination / response to UV / pyrimidine dimer repair / DNA replication-dependent nucleosome assembly / telomere organization / nucleosome => GO:0000786 / innate immune response in mucosa / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing / regulation of gene silencing by miRNA / nuclear chromosome / proteasomal protein catabolic process / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, DNA duplex unwinding / DNA-templated transcription, initiation / nucleotide-excision repair / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / nucleotide-excision repair, DNA incision, 5'-to lesion / regulation of megakaryocyte differentiation / DNA damage response, detection of DNA damage / nucleosome assembly / positive regulation of protein catabolic process / nucleotide-excision repair, DNA incision / regulation of circadian rhythm / protein-macromolecule adaptor activity / lipopolysaccharide binding / nucleosome / transcription-coupled nucleotide-excision repair / rhythmic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell junction / double-strand break repair via nonhomologous end joining / post-translational protein modification / chromatin organization / protein polyubiquitination / chromosome, telomeric region => GO:0000781 / ubiquitin-dependent protein catabolic process / Wnt signaling pathway / killing of cells of other organism / antibacterial humoral response / damaged DNA binding / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / protein ubiquitination / protein deubiquitination / cadherin binding / defense response to Gram-negative bacterium / protein heterodimerization activity / defense response to Gram-positive bacterium / negative regulation of cell population proliferation / chromatin => GO:0000785 / DNA repair / protein domain specific binding / cellular response to DNA damage stimulus / protein-containing complex binding / cellular protein metabolic process / viral process / negative regulation of apoptotic process / host cell nucleus / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
WD40-repeat-containing domain / Histone H3/CENP-A / WD40 repeat / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Histone H2A/H2B/H3 / Histone-fold / WD40/YVTN repeat-like-containing domain superfamily ...WD40-repeat-containing domain / Histone H3/CENP-A / WD40 repeat / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Histone H2A/H2B/H3 / Histone-fold / WD40/YVTN repeat-like-containing domain superfamily / WD40 repeat, conserved site / Histone H4, conserved site / DNA damage-binding protein 1 / Histone H2A, C-terminal domain / Histone H2A conserved site / DNA damage-binding protein 2 / CENP-T/Histone H4, histone fold / WD40-repeat-containing domain superfamily / Histone H2B
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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.
Validation ReportPDB-ID: 6r90

SummaryFull reportAbout validation report
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: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r90
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4764.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: 3.5 / Movie #1: 3.5
Minimum - Maximum-9.876421 - 27.450775
Average (Standard dev.)-0.003245564 (±0.7673506)
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
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-9.87627.451-0.003

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Supplemental data

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Sample components

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Entire UV-DDB bound to a THF2 containing nucleosome class A

EntireName: UV-DDB bound to a THF2 containing nucleosome class A / Number of components: 13

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Component #1: protein, UV-DDB bound to a THF2 containing nucleosome class A

ProteinName: UV-DDB bound to a THF2 containing nucleosome class A / Recombinant expression: No
MassTheoretical: 199 kDa

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Component #2: protein, Histone H3.1, Histone H2A, Histone H2B

ProteinName: Histone H3.1, Histone H2A, Histone H2BHistone H3 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, Histone H4

ProteinName: Histone H4 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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, DNA damage-binding protein 1(2), DNA damage-binding protein 2

ProteinName: DNA damage-binding protein 1(2), DNA damage-binding protein 2
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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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: 2 / 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: 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)(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)
MassTheoretical: 44.756648 kDa
SourceSpecies: Homo sapiens (human)

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

nucleic acidName: Human alpha-satellite DNA (145-MER) with abasic sites at positions 93-94
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)(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)(3DR)(3DR)(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: 44.452434 kDa
SourceSpecies: Homo sapiens (human)

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Component #12: protein, DNA damage-binding protein 1

ProteinName: DNA damage-binding protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 129.766305 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #13: protein, DNA damage-binding protein 2

ProteinName: DNA damage-binding protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.601844 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: 128763
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / 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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