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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4765 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of NCP_THF2(-3)-UV-DDB | ||||||||||||||||||||||||
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![]() | UV-DDB bound to a THF2 (-3) containing nucleosome
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||||||||
![]() | Matsumoto S / Cavadini S / Bunker RD / Thoma NH | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 Report | ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
Related structure data | ![]() 6r91CM ![]() 4762C ![]() 4763C ![]() 4764C ![]() 4766C ![]() 4767C ![]() 4768C ![]() 6r8yC ![]() 6r8zC ![]() 6r90C ![]() 6r92C ![]() 6r93C ![]() 6r94C C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire UV-DDB bound to a THF2 (-3) containing nucleosome
+Component #1: protein, UV-DDB bound to a THF2 (-3) containing nucleosome
+Component #2: protein, Histone H3.1, Histone H2A, Histone H2B
+Component #3: protein, Histone H4
+Component #4: protein, DNA
+Component #5: protein, DNA damage-binding protein 1(2), DNA damage-binding protein 2
+Component #6: protein, Histone H3.1
+Component #7: protein, Histone H4
+Component #8: protein, Histone H2A type 1-B/E
+Component #9: protein, Histone H2B type 1-J
+Component #10: nucleic-acid, Human alpha-satellite DNA (145-MER)
+Component #11: nucleic-acid, Human alpha-satellite DNA (145-MER) with abasic sit...
+Component #12: protein, DNA damage-binding protein 1
+Component #13: protein, DNA damage-binding protein 2
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Temperature: 277 K / Humidity: 85 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
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Image processing
![]() | Method: ![]() |
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3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF |
-Atomic model buiding
Modeling #1 | Refinement 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 |
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Output model |