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- EMDB-4765: Cryo-EM structure of NCP_THF2(-3)-UV-DDB -

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Basic information

Entry
Database: EMDB / ID: EMD-4765
TitleCryo-EM structure of NCP_THF2(-3)-UV-DDB
Map data
SampleUV-DDB bound to a THF2 (-3) containing nucleosome
  • 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 / 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 / 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 / biological process involved in 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / DNA replication-independent nucleosome assembly / telomere capping / regulation of mitotic cell cycle phase transition / interleukin-7-mediated signaling pathway / protein autoubiquitination / positive regulation of viral genome replication / response to UV / pyrimidine dimer repair / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / nucleosome => GO:0000786 / innate immune response in mucosa / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing / nucleotide-excision repair / regulation of gene silencing by miRNA / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, DNA duplex unwinding / nuclear chromosome / proteasomal protein catabolic process / DNA-templated transcription, initiation / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / nucleotide-excision repair, DNA incision, 5'-to lesion / regulation of megakaryocyte differentiation / positive regulation of protein catabolic process / nucleotide-excision repair, DNA incision / nucleosome assembly / DNA damage response, detection of DNA damage / lipopolysaccharide binding / protein-macromolecule adaptor activity / regulation of circadian rhythm / 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 / chromosome, telomeric region => GO:0000781 / chromatin organization / post-translational protein modification / protein polyubiquitination / Wnt signaling pathway / ubiquitin-dependent protein catabolic process / 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 / chromatin => GO:0000785 / negative regulation of cell population proliferation / DNA repair / protein domain specific binding / cellular response to DNA damage stimulus / cellular protein metabolic process / protein-containing complex binding / viral process / negative regulation of apoptotic process / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Histone H3/CENP-A / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / 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 ...Histone H3/CENP-A / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / 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 / 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: 4.1 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 ReportSummary, Full report, XML, About 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: 5.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r91
  • Surface level: 5.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4765.png

Downloads & links

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Map

FileDownload / File: emd_4765.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.72 Å/pix.
x 192 pix.
= 330.24 Å		1.72 Å/pix.
x 192 pix.
= 330.24 Å		1.72 Å/pix.
x 192 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.12 / Movie #1: 5.12
Minimum - Maximum-19.132261 - 45.49785
Average (Standard dev.)-0.0000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z330.240330.240330.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-19.13245.498-0.000

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Supplemental data

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Sample components

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Entire UV-DDB bound to a THF2 (-3) containing nucleosome

EntireName: UV-DDB bound to a THF2 (-3) containing nucleosome / Number of components: 13

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Component #1: protein, UV-DDB bound to a THF2 (-3) containing nucleosome

ProteinName: UV-DDB bound to a THF2 (-3) containing nucleosome / Recombinant expression: No

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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 97-98
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)(DG)(DA)(DT)(DG)(3DR)(3DR)(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 solutionpH: 7.4
VitrificationCryogen 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
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 119309
3D reconstructionResolution: 4.1 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

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

6r91

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