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- EMDB-65387: Structure of the bacteriophage E1004 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-65387
TitleStructure of the bacteriophage E1004 capsid
Map data
Sample
  • Complex: Escherichia phage
    • Protein or peptide: Minor capsid protein
KeywordsComplex / VIRAL PROTEIN
Biological speciesEscherichia phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsSun BN / 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: Structure / Year: 2025
Title: Cryo-EM structure of drug-resistant Escherichia coli phage E1004 reveals a conserved cylindrical core among podophages.
Authors: Binning Sun / Jing Zheng / Yuan Fu / Fengyuan Tian / Hao Xiao / Su Li / Lingpeng Cheng / Ping Chen / Hongrong Liu /
Abstract: Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution ...Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution structures of near-complete cores remain scarce. Here, we present the near-atomic-resolution cryo-electron microscopy (cryo-EM) structure of the drug-resistant E. coli phage E1004, which features a T7-like core-portal-tail structure with six P22-like tailspikes. We found that the cylindrical core comprises four proteins: gp17, gp27, gp28, and gp29. Gp29 forms a tetramer, while gp28 and gp27 assemble into octamers. Notably, there are sixteen copies of gp17 in two conformations, distinct from the small core protein gp6.7 in T7. The gp17-gp27 complex reveals the mechanism for mediating the symmetry adjustment at the core-portal interface. Moreover, comparative analysis with other podophage cores highlights diversity in core protein composition and organization, particularly among the small core proteins. We propose that these variations represent evolutionary adaptations to diverse host envelopes.
History
DepositionJul 16, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65387.png

Downloads & links

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Map

FileDownload / File: emd_65387.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 800 pix.
= 880. Å		1.1 Å/pix.
x 800 pix.
= 880. Å		1.1 Å/pix.
x 800 pix.
= 880. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.3698143 - 0.95004123
Average (Standard dev.)0.0017561446 (±0.062197343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-399-399-399
Dimensions800800800
Spacing800800800
CellA=B=C: 880.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65387_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65387_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage

EntireName: Escherichia phage (virus)
Components
  • Complex: Escherichia phage
    • Protein or peptide: Minor capsid protein

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Supramolecule #1: Escherichia phage

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

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Macromolecule #1: Minor capsid protein

MacromoleculeName: Minor capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 36.084027 KDa
SequenceString: MANVPGQKVG TDQGKGKSGS DALALFLKVF AGEVLTAFTR RSVTADKHIV RTIQNGKSAQ FPVMGRTSGV YLAPGERLSD KRKGIKHTE KNITIDGLLT ADVMIFDIED AMNHYDVAGE YSNQLGEALA IAADGAVLAE MAILCNLPAA SNENIAGLGT A SVLEVGKK ...String:
MANVPGQKVG TDQGKGKSGS DALALFLKVF AGEVLTAFTR RSVTADKHIV RTIQNGKSAQ FPVMGRTSGV YLAPGERLSD KRKGIKHTE KNITIDGLLT ADVMIFDIED AMNHYDVAGE YSNQLGEALA IAADGAVLAE MAILCNLPAA SNENIAGLGT A SVLEVGKK ADLNTPAKLG EAIIGQLTIA RAKLTSNYVP AGDRYFYTTP DNYSAILAAL MPNAANYAAL IDPETGNIRN VM GFVVVEV PHLVQGGAGG TRGADGISIA SGQKHAFPAT AAGAVKVAMD NVVGLFSHRS AVGTVKLRDL ALERDRDVDA QGD LIVGKY AMGHGGLRPE AAGALVFSPA 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: FEI FALCON IV (4k 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: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 63726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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