[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

TitleHuman 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations.
Journal, issue, pagesCommun Biol, Vol. 7, Issue 1, Page 1202, Year 2024
Publish dateSep 28, 2024
AuthorsQinglong You / Xiang Feng / Yi Cai / Stephen B Baylin / Huilin Li /
PubMed AbstractThe human glycosylase OGG1 extrudes and excises the oxidized DNA base 8-oxoguanine (8-oxoG) to initiate base excision repair and plays important roles in many pathological conditions such as cancer, ...The human glycosylase OGG1 extrudes and excises the oxidized DNA base 8-oxoguanine (8-oxoG) to initiate base excision repair and plays important roles in many pathological conditions such as cancer, inflammation, and neurodegenerative diseases. Previous structural studies have used a truncated protein and short linear DNA, so it has been unclear how full-length OGG1 operates on longer DNA or on nucleosomes. Here we report cryo-EM structures of human OGG1 bound to a 35-bp long DNA containing an 8-oxoG within an unmethylated Cp-8-oxoG dinucleotide as well as to a nucleosome with an 8-oxoG at super-helical location (SHL)-5. The 8-oxoG in the linear DNA is flipped out by OGG1, consistent with previous crystallographic findings with a 15-bp DNA. OGG1 preferentially binds near dsDNA ends at the nucleosomal entry/exit sites. Such preference may underlie the enzyme's function in DNA double-strand break repair. Unexpectedly, we find that OGG1 bends the nucleosomal entry DNA, flips an undamaged guanine, and binds to internal nucleosomal DNA sites such as SHL-5 and SHL+6. We suggest that the DNA base search mechanism by OGG1 may be chromatin context-dependent and that OGG1 may partner with chromatin remodelers to excise 8-oxoG at the nucleosomal internal sites.
External linksCommun Biol / PubMed:39341999 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 7.6 Å
Structure data

43607

8vx4

EMDB-43607, PDB-8vx4:
Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle
Method: EM (single particle) / Resolution: 3.7 Å

43608

8vx5

EMDB-43608, PDB-8vx5:
Nucleosome core particle containing an 8-oxoG damage site
Method: EM (single particle) / Resolution: 3.3 Å

43609

8vx6

EMDB-43609, PDB-8vx6:
Human OGG1 bound at the nucleosomal DNA entry site
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-43610: Human OGG1 bound at the nucleosomal super helical location -5
Method: EM (single particle) / Resolution: 5.7 Å

EMDB-43611: Human OGG1 bound at the nucleosomal super helical location +6
Method: EM (single particle) / Resolution: 7.6 Å

Source
  • homo sapiens (human)
  • synthetic construct (others)
  • xenopus laevis (African clawed frog)
KeywordsHYDROLASE / LYASE/DNA / Human OGG1 binding at 8-oxoG of a 35 bp DNA duplex / LYASE-DNA complex / STRUCTURAL PROTEIN/DNA / Nucleosome core particle containing 8-oxoG DNA damage / STRUCTURAL PROTEIN-DNA complex / LYASE/STRUCTURAL PROTEIN/DNA / LYASE-STRUCTURAL PROTEIN-DNA complex

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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