[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

TitleStructural basis for DNA proofreading.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 8501, Year 2023
Publish dateDec 27, 2023
AuthorsGina Buchel / Ashok R Nayak / Karl Herbine / Azadeh Sarfallah / Viktoriia O Sokolova / Angelica Zamudio-Ochoa / Dmitry Temiakov /
PubMed AbstractDNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base ...DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement of the mismatched base into the exonuclease site. Altogether, our findings suggest a conserved 'bolt-action' mechanism of proofreading based on iterative cycles of DNAP translocation without dissociation from the DNA, facilitating primer transfer between catalytic sites. Functional assays and mutagenesis corroborate this mechanism, connecting pathogenic mutations to crucial structural elements in proofreading steps.
External linksNat Commun / PubMed:38151585 / PubMed Central
MethodsEM (single particle)
Resolution2.58 - 3.08 Å
Structure data

29745

8g5i

EMDB-29745, PDB-8g5i:
Cryo-EM structure of the Mismatch Sensing Complex (I) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.75 Å

29746

8g5j

EMDB-29746, PDB-8g5j:
Cryo-EM structure of the Mismatch Uncoupling Complex (II) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.63 Å

29747

8g5k

EMDB-29747, PDB-8g5k:
Cryo-EM structure of the Wedge Alignment Complex (VIII) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.9 Å

29748

8g5l

EMDB-29748, PDB-8g5l:
Cryo-EM structure of the Primer Separation Complex (IX) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 3.0 Å

29749

8g5m

EMDB-29749, PDB-8g5m:
Cryo-EM structure of the Mismatch Locking Complex (III) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.58 Å

29750

8g5n

EMDB-29750, PDB-8g5n:
Cryo-EM structure of the Guide loop Engagement Complex (VI) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.73 Å

29751

8g5o

EMDB-29751, PDB-8g5o:
Cryo-EM structure of the Guide loop Engagement Complex (IV) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.61 Å

29752

8g5p

EMDB-29752, PDB-8g5p:
Cryo-EM structure of the Guide loop Engagement Complex (V) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 2.78 Å

41091

8t7e

EMDB-41091, PDB-8t7e:
Cryo-EM structure of the Backtracking Initiation Complex (VII) of Human Mitochondrial DNA Polymerase Gamma
Method: EM (single particle) / Resolution: 3.08 Å

Source
  • homo sapiens (human)
  • synthetic construct (others)
  • synthetic rna (others)
KeywordsREPLICATION/DNA / Mitochondrial DNA Polymerase / DNA Proofreading / Mismatch Sensing / REPLICATION / REPLICATION-DNA complex / PolG / Wedge alignment / Primer Separation / REPLICATION/DNA/RNA / Mismatch Locking / REPLICATION-DNA-RNA complex / Guide loop Engagement / Transferase/DNA / Backtracking / Mismatch repair / 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