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- PDB-9x3o: Phage T4 neck in post-tail-contraction state (genome-full particle) -

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Basic information

Entry
Database: PDB / ID: 9x3o
TitlePhage T4 neck in post-tail-contraction state (genome-full particle)
Components
  • Fibritin
  • Neck protein gp13
  • Neck protein gp14
  • Portal protein
  • Tail completion protein gp15
KeywordsVIRAL PROTEIN / Bacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / viral portal complex / viral genome packaging / viral release from host cell / virion component / host cell plasma membrane
Similarity search - Function
Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Portal protein Gp20 / Bacteriophage T4, Gp14, neck protein / : / Bacteriophage T4-like portal protein (Gp20) / Virus neck protein / Bacteriophage T4 neck protein gp13 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Neck protein gp13 / Neck protein gp14 / Tail completion protein gp15 / Portal protein
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsShao, Q. / Dong, J. / Wang, A. / Hu, H. / Yue, J. / Li, H. / Li, Y. / Zhang, Q. / Liu, J. / Sun, L. ...Shao, Q. / Dong, J. / Wang, A. / Hu, H. / Yue, J. / Li, H. / Li, Y. / Zhang, Q. / Liu, J. / Sun, L. / Fokine, A. / Rao, V.B. / Tao, P. / Fang, Q.
Funding support China, United States, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371285 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175340 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DP1DA060580 United States
National Science Foundation (NSF, United States)MCB-0923873 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110243 United States
National Institutes of Health/Office of the Director1S10OD023603-01A1 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Cryo-EM Structures of Phage T4 Infection Intermediate.
Authors: Qianqian Shao / Junhua Dong / Aohan Wang / Hongli Hu / Jian Yue / Hongmei Li / Yinyin Li / Qinfen Zhang / Jun Liu / Lei Sun / Andrei Fokine / Venigalla B Rao / Pan Tao / Qianglin Fang /
Abstract: Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. ...Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. Here, we capture a pre-genome-release intermediate of myophage T4 and determine its structure by cryo-electron microscopy. Comparative analysis of this tail-contracted, pre-genome-release intermediate structure with the mature T4 virion and the tail-contracted, post-genome-release structure reveals structural transitions in the tail, tape-measure protein (TMP), baseplate, and long tail fibers that drive genome delivery. Our findings further suggest that tail sheath contraction is coupled to a coordinated repositioning of the viral DNA-TMP complex, potentially facilitating genome translocation via charge-mediated interactions. It appears that the expelled TMP may further reorganize into a putative transmembrane complex that supports genome delivery into the host cytosol.
History
DepositionOct 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Neck protein gp13
D: Neck protein gp13
E: Neck protein gp14
F: Tail completion protein gp15
G: Fibritin
H: Fibritin
I: Fibritin
J: Fibritin
K: Fibritin
L: Fibritin


Theoretical massNumber of molelcules
Total (without water)564,41912
Polymers564,41912
Non-polymers00
Water00
1
A: Portal protein
B: Portal protein
C: Neck protein gp13
D: Neck protein gp13
E: Neck protein gp14
F: Tail completion protein gp15
G: Fibritin
H: Fibritin
I: Fibritin
J: Fibritin
K: Fibritin
L: Fibritin
x 6


Theoretical massNumber of molelcules
Total (without water)3,386,51372
Polymers3,386,51372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Portal protein / Gene product 20 / gp20


Mass: 61117.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13334
#2: Protein Neck protein gp13 / Gene product 13 / gp13


Mass: 34772.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P11110
#3: Protein Neck protein gp14 / Gene product 14 / gp14


Mass: 29597.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P11111
#4: Protein Tail completion protein gp15 / Gene product 15 / gp15 / Tail connector protein 15 / Tail terminator protein


Mass: 31587.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P11112
#5: Protein
Fibritin / Collar protein / Whisker antigen control protein


Mass: 51909.164 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10104
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 T4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
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: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Detector modeFilm or detector modelNum. of real images
11840SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)2276
21859.6GATAN K3 (6k x 4k)5090
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scans
Movie frames/imageIDImage recording-IDEntry-ID
32119X3O
229X3O

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
12RELION3.13D reconstruction
13PHENIX1.19.2_4158model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 116671
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40108 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00220057
ELECTRON MICROSCOPYf_angle_d0.48527127
ELECTRON MICROSCOPYf_dihedral_angle_d3.7732654
ELECTRON MICROSCOPYf_chiral_restr0.0422969
ELECTRON MICROSCOPYf_plane_restr0.0043553

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