[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

TitlePolγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 6, Page 812-823, Year 2023
Publish dateMay 18, 2023
AuthorsJoon Park / Geoffrey K Herrmann / Patrick G Mitchell / Michael B Sherman / Y Whitney Yin /
PubMed AbstractAccurate replication of mitochondrial DNA (mtDNA) by DNA polymerase γ (Polγ) is essential for maintaining cellular energy supplies, metabolism, and cell cycle control. To illustrate the structural ...Accurate replication of mitochondrial DNA (mtDNA) by DNA polymerase γ (Polγ) is essential for maintaining cellular energy supplies, metabolism, and cell cycle control. To illustrate the structural mechanism for Polγ coordinating polymerase (pol) and exonuclease (exo) activities to ensure rapid and accurate DNA synthesis, we determined four cryo-EM structures of Polγ captured after accurate or erroneous incorporation to a resolution of 2.4-3.0 Å. The structures show that Polγ employs a dual-checkpoint mechanism to sense nucleotide misincorporation and initiate proofreading. The transition from replication to error editing is accompanied by increased dynamics in both DNA and enzyme, in which the polymerase relaxes its processivity and the primer-template DNA unwinds, rotates, and backtracks to shuttle the mismatch-containing primer terminus 32 Å to the exo site for editing. Our structural and functional studies also provide a foundation for analyses of Polγ mutation-induced human diseases and aging.
External linksNat Struct Mol Biol / PubMed:37202477 / PubMed Central
MethodsEM (single particle)
Resolution2.46 - 3.04 Å
Structure data

27154

8d33

EMDB-27154, PDB-8d33:
Human mitochondrial DNA polymerase gamma ternary complex with GC basepair
Method: EM (single particle) / Resolution: 2.46 Å

27155

8d37

EMDB-27155, PDB-8d37:
Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in replication conformer
Method: EM (single particle) / Resolution: 2.65 Å

27163

8d3r

EMDB-27163, PDB-8d3r:
Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in intermediate conformer
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-27169: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (consensus)
Method: EM (single particle) / Resolution: 2.91 Å

EMDB-27170: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (local refinement of subunit A and primer/template DNA)
Method: EM (single particle) / Resolution: 2.76 Å

EMDB-27171: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (local refinement of subunit B)
Method: EM (single particle) / Resolution: 2.76 Å

27172

8d42

EMDB-27172, PDB-8d42:
Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (composite)
Method: EM (single particle) / Resolution: 2.91 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE/DNA / DNA-binding protein / DNA polymerase / TRANSFERASE-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://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