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- EMDB-65480: Cryo-EM structure of bacteriophage P1 baseplate in C3 -

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Basic information

Entry
Database: EMDB / ID: EMD-65480
TitleCryo-EM structure of bacteriophage P1 baseplate in C3
Map data
Sample
  • Complex: Escherichia phage P1
    • Protein or peptide: Gp6
    • Protein or peptide: PmgG
    • Protein or peptide: PmgA
    • Protein or peptide: Tub
    • Protein or peptide: BplA
    • Protein or peptide: Gp26
    • Protein or peptide: Gp16
    • Protein or peptide: Gp5
Keywordsbaseplate / phage / VIRAL PROTEIN
Biological speciesEscherichia phage P1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen Y / 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
DepositionJul 22, 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_65480.png

Downloads & links

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Map

FileDownload / File: emd_65480.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. 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: 0.49
Minimum - Maximum-0.29376805 - 1.2403518
Average (Standard dev.)0.021159237 (±0.09063546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65480_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_65480_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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: Gp6
    • Protein or peptide: PmgG
    • Protein or peptide: PmgA
    • Protein or peptide: Tub
    • Protein or peptide: BplA
    • Protein or peptide: Gp26
    • Protein or peptide: Gp16
    • Protein or peptide: Gp5

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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: Gp6

MacromoleculeName: Gp6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 37.26132 KDa
SequenceString: MATKTTTAPE TDSKRTQLFL QSVSIGQNEI PREMIVGCTY VEPGELSGPQ LMLMIRDSTA YVVNKLGVKF GTILTVSLGD PEGHGGILF SEEFFVLKAP RKDDTVLIYA FSNPVRLLKV PSTSAQYFVD KPPSAVVSSL APGLKVNADS FRKTSTYHLN V GEKPTKVL ...String:
MATKTTTAPE TDSKRTQLFL QSVSIGQNEI PREMIVGCTY VEPGELSGPQ LMLMIRDSTA YVVNKLGVKF GTILTVSLGD PEGHGGILF SEEFFVLKAP RKDDTVLIYA FSNPVRLLKV PSTSAQYFVD KPPSAVVSSL APGLKVNADS FRKTSTYHLN V GEKPTKVL QEIARDTGSM CWASRGMINF KSMEKMANAA PSLTYESANP NTSGFTISQF NILNADYEYQ RRHNYRMASY DM TKGVVYS GNQEDPIKFT SNPDPTALAN YNKFILPRLD MLVEGNAALT PGTTLKIVVH NTAGDGELDE SIPDKMIVMS VTH FEDRFR FVSRAQLGVV NG

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Macromolecule #2: PmgG

MacromoleculeName: PmgG / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 20.578162 KDa
SequenceString: MAPIAYGVYS QADGVSPYLK VTLTNSQYQV TGYISQGAAM NMAQNWEAPF TGMSMGSVSG ALGGFVQVGT ETTSVARWNS LMVWEGGTP PTFTLPVTFI ALNNPFIEVS GAIAALTAMI SPELKAANVG GQIPERVTLN IGRRINITDV AIQDLSFDLD A PRDSNGYF ...String:
MAPIAYGVYS QADGVSPYLK VTLTNSQYQV TGYISQGAAM NMAQNWEAPF TGMSMGSVSG ALGGFVQVGT ETTSVARWNS LMVWEGGTP PTFTLPVTFI ALNNPFIEVS GAIAALTAMI SPELKAANVG GQIPERVTLN IGRRINITDV AIQDLSFDLD A PRDSNGYF LKNTVNLQLT GSSIYNSSDI VRAFQ

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Macromolecule #3: PmgA

MacromoleculeName: PmgA / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 13.24991 KDa
SequenceString:
MANNNEIDPL LTLELSGVKT YESQEEAWGA RLYEWLNTYQ GEVYGDPSWG NVLPQFKHEP TNLSHVQIAV EAMLLQKLTV DLPDIPISG LSVAEGDAFD KLKISIRIRD ITITQDVVL

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Macromolecule #4: Tub

MacromoleculeName: Tub / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 22.335309 KDa
SequenceString: MGLNVASVKS YVSSALTTTL FGSGVGEREV GKLTSIIMNK MLFAQGWQFS VEVDGLEGAD FFAKDITYHD YSIEYETIKI GGGNILQPT ERSPGQITMM VRDTVDGLVL DWFKTAKSRV INPDGTGNIP SQYLLNVRIY RLLSSGLTKL ENEMTVFPVT T GDVTYARD ...String:
MGLNVASVKS YVSSALTTTL FGSGVGEREV GKLTSIIMNK MLFAQGWQFS VEVDGLEGAD FFAKDITYHD YSIEYETIKI GGGNILQPT ERSPGQITMM VRDTVDGLVL DWFKTAKSRV INPDGTGNIP SQYLLNVRIY RLLSSGLTKL ENEMTVFPVT T GDVTYARD QVTEFKSFPM TFALHSTFNQ SSSSLASLLG FSFSL

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Macromolecule #5: BplA

MacromoleculeName: BplA / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 53.624277 KDa
SequenceString: MSKTTPTKDS IRAEFEELVE KDSFWSKFVG SQFVSMLTLF ITQIVYRCFQ YADAALAEGF ISTATRRSSI LAAAETNSYV GTKPTPSSG MIEITATSED APAVIPKNMP LISDDQYPYM TMDVCRLVDG TGTVEVAQLE IQEVTYTVTA AKEFLEVVLS K ALTAVCYK ...String:
MSKTTPTKDS IRAEFEELVE KDSFWSKFVG SQFVSMLTLF ITQIVYRCFQ YADAALAEGF ISTATRRSSI LAAAETNSYV GTKPTPSSG MIEITATSED APAVIPKNMP LISDDQYPYM TMDVCRLVDG TGTVEVAQLE IQEVTYTVTA AKEFLEVVLS K ALTAVCYK LEVFVTTDGK TTQWSSSTMF RLAGSKSQVY VEFYKPSEQL GVRFGDGLIG QIPPEGSTIT LKVWCTNGDI TL VAGQNLT PVDSAANLAN LISVKTTTPI TAGTDAETTE ITRNRAQYYL AYDDQVVWGG DYTYFLVRNI PGLSWVKAWG EGQ QEKLDG AYNVQNINKI FISGWHPNKS QSELEEMILA AFKKVPNELN KKFSYKEVRK LPFKITITGR ISASLTIENV TDEL KSALE TKFGRDSTFF DPNRVGKYIL IKKKDVWAFI ETLGYFRDFY LEFVEWNESN GFYDFVYLDT ENSTFNISYE EE

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Macromolecule #6: Gp26

MacromoleculeName: Gp26 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 14.472648 KDa
SequenceString:
MATSITTTQS TRQYPLSRYD DRNIADPILR AELRKEVMLM CESNDKNLTI YYVLPDEQYR PDLLAYRMWG IAELRWVVTL AAGLEDESQ GMTVGKKLKL PPATWIREMI RHFQYDGQVI GTLSIA

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Macromolecule #7: Gp16

MacromoleculeName: Gp16 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 31.38759 KDa
SequenceString: MQRSWFNHRL TSAKQKSLLY KSLADLVQSM MDTFVDPWLE RITNRKSIFS MSKEDLETRT NELGQFFTIR TSNSSSVPML LQQRLDEIH FKGTERPINQ TIYREFNGIS VLWDPIYAPV DLERHPYGTV LIPESTLETT GGTFGEMFLT SRGMISIPIN D LARTMGIT ...String:
MQRSWFNHRL TSAKQKSLLY KSLADLVQSM MDTFVDPWLE RITNRKSIFS MSKEDLETRT NELGQFFTIR TSNSSSVPML LQQRLDEIH FKGTERPINQ TIYREFNGIS VLWDPIYAPV DLERHPYGTV LIPESTLETT GGTFGEMFLT SRGMISIPIN D LARTMGIT GTIDQSAITE EILRKFNQFV KPLLPLHIVF DGLTLYLSVV VNEHADMITL NEISDTEKAY CWFETSDTTS LT GVTSISA PITATPGGTI VKATPTFDRT RADDLLLDSD A

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Macromolecule #8: Gp5

MacromoleculeName: Gp5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage P1 (virus)
Molecular weightTheoretical: 21.68734 KDa
SequenceString: MGSLTGKYRA VVISVDDPKG LMRTQIRVVG MMDGLPDASL PWAEAILSNA NTFSPFLPGD KVWVEFPYNG DSRWPLIIGY AQDASGGAP NVPPEASGQG EGYVPPEVEG APAQPSTSAK KDFISSRNGL MEIRTAGGAW AVTHLKSGTT IGFNEAGELY A ISQGPAFI ...String:
MGSLTGKYRA VVISVDDPKG LMRTQIRVVG MMDGLPDASL PWAEAILSNA NTFSPFLPGD KVWVEFPYNG DSRWPLIIGY AQDASGGAP NVPPEASGQG EGYVPPEVEG APAQPSTSAK KDFISSRNGL MEIRTAGGAW AVTHLKSGTT IGFNEAGELY A ISQGPAFI SSAGNLDIKS GADVALKAGG SMAIEASGNL SIKAAQVSVD KA

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30339
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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