[English] 日本語
Yorodumi
- EMDB-52709: Enterobacteriaphage PRD1 - P12 protein filament in complex with r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52709
TitleEnterobacteriaphage PRD1 - P12 protein filament in complex with repetitive (ATGCT) ssDNA
Map dataPrimary Map
Sample
  • Complex: P12 filament bound to ssDNA
    • Protein or peptide: Enterobacteriaphage PRD1 - P12 protein filament
    • DNA: ssDNA repetitive (ATGCT)x16
KeywordsSSB / Protein primed replication / PRD1 / Protein filament / Homooligomer / ssDNA-binding / REPLICATION
Function / homologynucleotide binding / DNA binding / Single-stranded DNA-binding protein
Function and homology information
Biological speciesEnterobacteria phage PRD1 (virus) / synthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsDegen M / Traeger KL / Hiller S
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss Nanoscience Institute 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
DepositionFeb 4, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52709.png

Downloads & links

-
Map

FileDownload / File: emd_52709.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0313
Minimum - Maximum-0.23103 - 0.3563239
Average (Standard dev.)0.000063146574 (±0.008158361)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: DeepEMhancer Map

Fileemd_52709_additional_1.map
AnnotationDeepEMhancer Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_52709_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_52709_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : P12 filament bound to ssDNA

EntireName: P12 filament bound to ssDNA
Components
  • Complex: P12 filament bound to ssDNA
    • Protein or peptide: Enterobacteriaphage PRD1 - P12 protein filament
    • DNA: ssDNA repetitive (ATGCT)x16

-
Supramolecule #1: P12 filament bound to ssDNA

SupramoleculeName: P12 filament bound to ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterobacteria phage PRD1 (virus)

-
Macromolecule #1: Enterobacteriaphage PRD1 - P12 protein filament

MacromoleculeName: Enterobacteriaphage PRD1 - P12 protein filament / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage PRD1 (virus)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MEIVSKLTLK TIGAQPKPHS VKENTALASI YGRVRGKKVG QSTFGDFIKF EGEFEGVNIA TGEVFRSGAL ILPKVLESLL AGAVDGENTV DFAVEIWAKP SEKGNTGYEY GVKPLIEPAA SDELAALRNQ VKAALPAPAA AGEAAAEAKP AAKAKAKAEA

UniProtKB: Single-stranded DNA-binding protein

-
Macromolecule #2: ssDNA repetitive (ATGCT)x16

MacromoleculeName: ssDNA repetitive (ATGCT)x16 / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATGCTATGCT ATGCTATGCT ATGCTATGCT ATGCTATGCT ATGCTATGCT ATGCTATGCT ATGCTATGCT ATGCTATGCT

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.11 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 28.281 Å
Applied symmetry - Helical parameters - Δ&Phi: 17.969 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 183109
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9gfq

Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

+
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