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- EMDB-64249: Cryo-EM structure of bacteriophage P1 head -

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Basic information

Entry
Database: EMDB / ID: EMD-64249
TitleCryo-EM structure of bacteriophage P1 head
Map data
Sample
  • Complex: Escherichia phage P1
    • Protein or peptide: Gp23
    • Protein or peptide: Hdf
    • Protein or peptide: Defense against restriction protein A
Keywordshead / phage / VIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYang F / Liu HR
Funding support China, 3 items
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, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64249.png

Downloads & links

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Map

FileDownload / File: emd_64249.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-4.3936086 - 11.759617
Average (Standard dev.)0.0042944564 (±0.6436035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64249_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64249_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage P1

EntireName: Escherichia phage P1 (virus)
Components
  • Complex: Escherichia phage P1
    • Protein or peptide: Gp23
    • Protein or peptide: Hdf
    • Protein or peptide: Defense against restriction protein A

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Supramolecule #1: Escherichia phage P1

SupramoleculeName: Escherichia phage P1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage P1 (virus)

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Macromolecule #1: Gp23

MacromoleculeName: Gp23 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 62.326352 KDa
SequenceString: MSNLREYQNR IADIAKRSKA VLGWASTAQF GTDNQFIKDD AARAASILEA ARKDPVFAGI SDNATAQIAT AWASALADYA AAHKSMPRP EILASCHQTL ENCLIESTRN SMDATNKAML ESVAAEMMSV SDGVMRLPLF LAMILPVQLG AATADACTFI P VTRDQSDI ...String:
MSNLREYQNR IADIAKRSKA VLGWASTAQF GTDNQFIKDD AARAASILEA ARKDPVFAGI SDNATAQIAT AWASALADYA AAHKSMPRP EILASCHQTL ENCLIESTRN SMDATNKAML ESVAAEMMSV SDGVMRLPLF LAMILPVQLG AATADACTFI P VTRDQSDI YEVFNVAGSS FGSYAAGDVL DMQSVGVYSQ LRRRYVLVAS SDGTSKTATF KMEDFEGQNV PIRKGRTNIY VN RIKSVVD NGSGSLLHSF TNAAGEQITV TCSLNYNIGQ IALSFSKAPD KGTEIAIETE INIEAAPELI PLINHEMKKY TLF PSQFVI AAEHTVQAAY EAQREFGLDL GSLQFRTLKE YLSHEQDMLR LRIMIWRTLA TDTFDIALPV NQSFDVWATI IRGK FQTVY RDIIERVKSS GAMGMFAGAD AASFFKQLPK DFFQPAEDYI QTPYVHYIGT LFGNVKVYEV PAGICKNLTT ENIQF SSMD VLCYVRDENP GKAGFVTGDA VPAIPFQHPT TPALVNRTTL WGSAINDMHP RNGADYFTRV TLTMAKKGGL NFISGD TID AGDSE

UniProtKB: Gp23

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Macromolecule #2: Hdf

MacromoleculeName: Hdf / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 22.189506 KDa
SequenceString: MCQMTKNKYA TVDFDQVNEK GLKSLITAIN KTGVTVIEVD SSNRATTKDG VKVKTAKLVL SDGQILAIQV NDTGDISSVK LNGKAIPNA QSPDIKTLGT VMGQAARKNS AKFQKSLIAK AKRVANPVDK KPAVKSNFQR LQEAKQRNAQ VVAAYKSAQN S VSFNQQQI ...String:
MCQMTKNKYA TVDFDQVNEK GLKSLITAIN KTGVTVIEVD SSNRATTKDG VKVKTAKLVL SDGQILAIQV NDTGDISSVK LNGKAIPNA QSPDIKTLGT VMGQAARKNS AKFQKSLIAK AKRVANPVDK KPAVKSNFQR LQEAKQRNAQ VVAAYKSAQN S VSFNQQQI TDLRAKLDKE TGRLNNEKAR NGELKRRLKQ LKAGN

UniProtKB: Hdf

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Macromolecule #3: Defense against restriction protein A

MacromoleculeName: Defense against restriction protein A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 69.550734 KDa
SequenceString: MEQFNINKGM TIKPGLDVLP PPVTDDEYRA LMAGEDRYLM TESNTLEEIE ATFFYDTPIH WCATDLLEAI SSTRLQLHRT MQAFVRALN QKLNGTGISA GSDKTGDVAQ SGARAIGGAE IGRARNVNGL PVLPAIIPLS DGQTISILFH SPTAENRITN S DTLVAFQF ...String:
MEQFNINKGM TIKPGLDVLP PPVTDDEYRA LMAGEDRYLM TESNTLEEIE ATFFYDTPIH WCATDLLEAI SSTRLQLHRT MQAFVRALN QKLNGTGISA GSDKTGDVAQ SGARAIGGAE IGRARNVNGL PVLPAIIPLS DGQTISILFH SPTAENRITN S DTLVAFQF LLNKKDVTHT VAPMSGRDMT LAQVTMKLAN LAEKNSAKFQ RAQKKKKALV DEITQLQADS DQKEDAMSDL AD QVAAVEG QKADLEQKIN AVASEADSLY EENERLQGEI DRLNRTGGRD TIAPAGMTGG HSRALTDRLA SIKNRMHMDG EAT LSNGAS MKQFIGDGEG YIQLTDPDGS VYMIKAKSIQ GVDMADAIGK LFKAYKAGNV SEYLVQPEEH KPENVEPESA EDTG SSSPE PEVSVGAYRY ALQMRPAAPG AIPEGNKAIL PRPDEGDPYY EYARYGIATY DTPLSDQQMS EYDLKLLPRE DSFDF LAKT LTNGPFGKYA QKALELATNS PDEFRVMLKT QFQKTFPNIA FPGGAGTEKM VQSMINALQA EVGEITQPEP APAQPD ETV SEADAEANKA IEYLNNVMDM QSTDMAEIRN ARGNVREAIA ALQTAGRFEE NEELVNGAAR HLADLLVAIQ KAGVAA

UniProtKB: Defense against restriction protein A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11800
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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