[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleDNA damage detection in nucleosomes involves DNA register shifting.
Journal, issue, pagesNature, Vol. 571, Issue 7763, Page 79-84, Year 2019
Publish dateMay 29, 2019
AuthorsSyota 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 /
PubMed AbstractAccess 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.
External linksPubMed:31142837 / Publisher's page
KeywordsCryoelectron Microscopy / DDB1 protein, human / DDB2 protein, human / DNA / DNA Damage / DNA-Binding Proteins / Histones / Humans / Models, Molecular / Nucleosomes / Pyrimidine Dimers / Thermodynamics / Ultraviolet Rays / pyrimidine-pyrimidone dimer / DNA BINDING PROTEIN / Nucleosome / 6-4 photoproduct / THF2 photoproduct
MethodsEM (single particle)
Resolution3.5 - 4.8 A
Structure data

EMDB-4762:
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB

EMDB-4763:
Cryo-EM structure of NCP_THF2(-1)-UV-DDB

EMDB-4764:
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A

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

EMDB-4766:
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B

EMDB-4767:
Cryo-EM structure of NCP-6-4PP

EMDB-4768:
Cryo-EM structure of NCP_THF2(-3)

PDB-6r8y:
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB

PDB-6r8z:
Cryo-EM structure of NCP_THF2(-1)-UV-DDB

PDB-6r90:
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A

PDB-6r91:
Cryo-EM structure of NCP_THF2(-3)-UV-DDB

PDB-6r92:
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B

PDB-6r93:
Cryo-EM structure of NCP-6-4PP

PDB-6r94:
Cryo-EM structure of NCP_THF2(-3)

Source
  • homo sapiens (human)

+
About Yorodumi Papers

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more