6R91

Cryo-EM structure of NCP_THF2(-3)-UV-DDB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

DNA damage detection in nucleosomes involves DNA register shifting.

Matsumoto, S.Cavadini, S.Bunker, R.D.Grand, R.S.Potenza, A.Rabl, J.Yamamoto, J.Schenk, A.D.Schubeler, D.Iwai, S.Sugasawa, K.Kurumizaka, H.Thoma, N.H.

(2019) Nature 571: 79-84

  • DOI: 10.1038/s41586-019-1259-3
  • Primary Citation of Related Structures:  
    6R8Y, 6R8Z, 6R90, 6R91, 6R92, 6R93, 6R94

  • PubMed 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 pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA ...

    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.


    Organizational Affiliation

    University of Basel, Basel, Switzerland. nicolas.thoma@fmi.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
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Find proteins for P04908 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
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Find proteins for P06899 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1K1163Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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Find proteins for Q16531 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 2L450Homo sapiensMutation(s): 0 
Gene Names: DDB2
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Find proteins for Q92466 (Homo sapiens)
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Human alpha-satellite DNA (145-MER)I145Homo sapiens
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Human alpha-satellite DNA (145-MER) with abasic sites at positions 97-98J145Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSII3_160734/1
European Union666068
European Commission667951
European Commission705354
Japan Society for the Promotion of ScienceJapanJP18H05534
Japan Society for the Promotion of ScienceJapanJP16H06307
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Other