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- PDB-9ukm: Cryo-EM structure of bacteriophage P1 head -

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Basic information

Entry
Database: PDB / ID: 9ukm
TitleCryo-EM structure of bacteriophage P1 head
Components
  • Defense against restriction protein A
  • Gp23
  • Hdf
KeywordsVIRAL PROTEIN / head / phage
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / viral capsid assembly / viral capsid / symbiont-mediated suppression of host innate immune response
Similarity search - Function
Defence against restriction A, N-terminal / Defence against restriction A, C-terminal / Defence against restriction A N-terminal / Defence against restriction A C-terminal
Similarity search - Domain/homology
Defense against restriction protein A / Hdf / Gp23
Similarity search - Component
Biological speciesEscherichia phage P1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYang, F. / Liu, H.R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: PLoS Pathog / Year: 2026
Title: Structure of defense against restriction proteins DarA and Hdf in phage P1 reveals a new molecular mechanism during phage assembly, infection and DNA ejection.
Authors: Jing Zheng / Yuan Chen / Siting Chen / Junquan Zhou / Hao Xiao / Fan Yang / Hongrong Liu /
Abstract: The continuous "arms race" between bacterial antiviral defense systems and phage anti-defense strategies drives evolutionary innovation. Previous study indicated that the defense against restriction ...The continuous "arms race" between bacterial antiviral defense systems and phage anti-defense strategies drives evolutionary innovation. Previous study indicated that the defense against restriction (Dar) proteins DarA and Hdf in myophage P1 are associated with the head morphogenesis. However, the structural information for these proteins was lacking, and the mechanisms by which they mediate head morphogenesis and protect phage DNA against bacterial defense systems remained poorly understood. Using cryo-electron microscopy (cryo-EM), we resolved the entire structures of extended P1 and contracted P1 with partial DNA, with the latter lacking the baseplate, as well as the head structure of contracted P1 without DNA. We identified the structural proteins for the P1, including the head, connector complex, and baseplate, which exhibited conserved properties among the majority of myophages with a simple baseplate. Notably, 55 DarA-Hdf pairs are attached to the inner surface of head at each penton-hexon junction in the extended P1 and contracted P1 with partial DNA. The DarA and Hdf together form a complex that is tightly bound to the capsid and interacts with the DNA. However, these pairs are absent in the contracted P1 without DNA. Based on our three states of P1, we hypothesis that these extensive interactions among DarA, Hdf, DNA, and head play crucial roles in mediating capsid assembly, enhancing capsid stability, and protecting phage DNA. Our results provide a structural basis for further exploration of the mechanism by which Dar proteins function during phage assembly, infection and DNA ejection. This molecular mechanism may be conserved among P1-like phages.
History
DepositionApr 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
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Revision 2.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp23
B: Gp23
C: Gp23
D: Gp23
E: Gp23
F: Gp23
G: Gp23
H: Hdf
I: Defense against restriction protein A


Theoretical massNumber of molelcules
Total (without water)528,0259
Polymers528,0259
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gp23 / major capsid protein


Mass: 62326.352 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Escherichia phage P1 (virus) / References: UniProt: Q71TM1
#2: Protein Hdf


Mass: 22189.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage P1 (virus) / References: UniProt: Q71TE2
#3: Protein Defense against restriction protein A / DarA


Mass: 69550.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage P1 (virus) / References: UniProt: O21970
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia phage P1 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage P1 (virus)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11800 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00527307
ELECTRON MICROSCOPYf_angle_d0.62437015
ELECTRON MICROSCOPYf_dihedral_angle_d4.3533723
ELECTRON MICROSCOPYf_chiral_restr0.0434195
ELECTRON MICROSCOPYf_plane_restr0.0044819

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