6R92

Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 remain ...

    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

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. nicolas.thoma@fmi.ch.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,University of Basel, Basel, Switzerland.,Biosignal Research Center, and Graduate School of Science, Kobe University, Kobe, Japan.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland. nicolas.thoma@fmi.ch.,Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 2
L
450Homo sapiensMutation(s): 0 
Gene Names: DDB2
Find proteins for Q92466 (Homo sapiens)
Go to Gene View: DDB2
Go to UniProtKB:  Q92466
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens)
Go to Gene View: HIST1H2AB HIST1H2AE
Go to UniProtKB:  P04908
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1,DNA damage-binding protein 1
K
1163Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 1
MoleculeChainsLengthOrganism
Human alpha-satellite DNA (145-MER)I145Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
Human alpha-satellite DNA (145-MER) with abasic sites at positions 93-94J145Homo sapiens
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
J
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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