[English] 日本語
Yorodumi
- PDB-9gfq: Structure of PRD1 SSB P12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gfq
TitleStructure of PRD1 SSB P12
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / SSB / PRD1 / protein-primed / DNA-binding
Function / homologynucleotide binding / DNA binding / Single-stranded DNA-binding protein
Function and homology information
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTraeger, L.K. / Huguenin-Dezot, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPZ00P3_202090 Switzerland
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12.
Authors: Lena K Träger / Morris Degen / Joana Pereira / Janani Durairaj / Raphael Dias Teixeira / Sebastian Hiller / Nicolas Huguenin-Dezot /
Abstract: 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 ...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.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)16,6711
Polymers16,6711
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7080 Å2
Unit cell
Length a, b, c (Å)36.434, 50.999, 56.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Single-stranded DNA-binding protein / Protein P12


Mass: 16671.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-117 / Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Gene: XII / Production host: Escherichia coli (E. coli) / References: UniProt: P17637
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: From Morpheus[1], Molecular Dimensions: 0.12 M monosaccharides (0.2M D-glucose; 0.2M D-mannose; 0.2M D-galactose; 0.2M L-fucose; 0.2M D-xylose; 0.2M N-acetyl-D-glucosamine), 0.1 M buffer ...Details: From Morpheus[1], Molecular Dimensions: 0.12 M monosaccharides (0.2M D-glucose; 0.2M D-mannose; 0.2M D-galactose; 0.2M L-fucose; 0.2M D-xylose; 0.2M N-acetyl-D-glucosamine), 0.1 M buffer system 3 (Tris [base]; BICINE) pH 8.5, and 37.5 % v/v precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.7→37.8 Å / Num. obs: 12325 / % possible obs: 99 % / Redundancy: 12.4 % / CC1/2: 0.99 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 595 / CC1/2: 0.5 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.21refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.259 --
Rwork0.228 --
obs-12325 99 %
Refinement stepCycle: LAST / Resolution: 1.7→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms884 0 0 58 942

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more