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- PDB-9v30: C12 portal complex of the bacteriophage E1004 -

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Basic information

Entry
Database: PDB / ID: 9v30
TitleC12 portal complex of the bacteriophage E1004
ComponentsPortal protein
KeywordsVIRAL PROTEIN / Complex
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEscherichia phage (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsSun, B.N. / 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: 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
DepositionMay 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Portal protein
H: Portal protein
I: Portal protein
A: Portal protein
J: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
L: Portal protein
F: Portal protein
G: Portal protein
E: Portal protein


Theoretical massNumber of molelcules
Total (without water)687,96812
Polymers687,96812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein / Head-to-tail connector


Mass: 57330.652 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: The sequence of organism Saccharomyces cerevisiae is not available during the biocuration, replaced by A0A1S6KVI5 temporarily.
Source: (natural) Escherichia phage (virus) / References: UniProt: A0A1S6KVI5
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 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
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: 1600 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54423 / Symmetry type: POINT
RefinementHighest resolution: 3.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00447921
ELECTRON MICROSCOPYf_angle_d0.57765059
ELECTRON MICROSCOPYf_dihedral_angle_d4.2696721
ELECTRON MICROSCOPYf_chiral_restr0.0437477
ELECTRON MICROSCOPYf_plane_restr0.0058605

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