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Open data
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Basic information
Entry | Database: PDB / ID: 6r92 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B | ||||||||||||||||||||||||
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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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
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Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Matsumoto, S. / Cavadini, S. / Bunker, R.D. / Thoma, N.H. | ||||||||||||||||||||||||
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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
-Related structure data
Related structure data | ![]() 4766CM ![]() 4762C ![]() 4763C ![]() 4764C ![]() 4765C ![]() 4767C ![]() 4768C ![]() 6r8yC ![]() 6r8zC ![]() 6r90C ![]() 6r91C ![]() 6r93C ![]() 6r94C C: citing same article ( M: map data used to model this data |
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Similar-shape strucutres |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Human alpha-satellite DNA (145- ... , 2 types, 2 molecules IJ
#1: DNA chain | Mass: 44756.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#2: DNA chain | Mass: 44452.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-DNA damage-binding protein ... , 2 types, 2 molecules LK
#3: Protein | Mass: 50601.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#8: Protein | Mass: 129766.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein , 4 types, 8 molecules AEBFCGDH
#4: Protein | ![]() Mass: 15719.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ Production host: ![]() ![]() ![]() #5: Protein | ![]() Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 Cell line (production host): JM109(DE3) / Production host: ![]() ![]() ![]() #6: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #7: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Source (natural) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: dev_3318: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48925 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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