[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 cooperative ssDNA binding by bacteriophage protein filament P12.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 5, Year 2025
Publish dateFeb 27, 2025
AuthorsLena K Träger / Morris Degen / Joana Pereira / Janani Durairaj / Raphael Dias Teixeira / Sebastian Hiller / Nicolas Huguenin-Dezot /
PubMed AbstractProtein-primed DNA replication is a unique mechanism, bioorthogonal to other known DNA replication modes. It relies on specialised single-stranded DNA (ssDNA)-binding proteins (SSBs) to stabilise ...Protein-primed DNA replication is a unique mechanism, bioorthogonal to other known DNA replication modes. It relies on specialised single-stranded DNA (ssDNA)-binding proteins (SSBs) to stabilise ssDNA intermediates by unknown mechanisms. Here, we present the structural and biochemical characterisation of P12, an SSB from bacteriophage PRD1. High-resolution cryo-electron microscopy reveals that P12 forms a unique, cooperative filament along ssDNA. Each protomer binds the phosphate backbone of 6 nucleotides in a sequence-independent manner, protecting ssDNA from nuclease degradation. Filament formation is driven by an intrinsically disordered C-terminal tail, facilitating cooperative binding. We identify residues essential for ssDNA interaction and link the ssDNA-binding ability of P12 to toxicity in host cells. Bioinformatic analyses place the P12 fold as a distinct branch within the OB-like fold family. This work offers new insights into protein-primed DNA replication and lays a foundation for biotechnological applications.
External linksNucleic Acids Res / PubMed:40052821 / PubMed Central
MethodsEM (helical sym.) / X-ray diffraction
Resolution1.7 - 3.71 Å
Structure data

52708

9i86

EMDB-52708, PDB-9i86:
Enterobacteriaphage PRD1 - P12 protein filament in complex with poly(dT) ssDNA
Method: EM (helical sym.) / Resolution: 2.75 Å

52709

9i86

EMDB-52709: Enterobacteriaphage PRD1 - P12 protein filament in complex with repetitive (ATGCT) ssDNA
PDB-9i86: Enterobacteriaphage PRD1 - P12 protein filament in complex with poly(dT) ssDNA
Method: EM (helical sym.) / Resolution: 3.11 Å

52710

9i86

EMDB-52710: Enterobacteriaphage PRD1 - P12 protein filament in complex with non-repetitive ssDNA
PDB-9i86: Enterobacteriaphage PRD1 - P12 protein filament in complex with poly(dT) ssDNA
Method: EM (helical sym.) / Resolution: 3.71 Å

PDB-9gfq:
Structure of PRD1 SSB P12
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • enterobacteria phage prd1 (virus)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / SSB / PRD1 / protein-primed / DNA-binding / REPLICATION / Protein primed replication / Protein filament / Homooligomer / ssDNA-binding

+
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