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- PDB-9x3p: Phage T4 sheath in post-tail-contraction state (genome-full particle) -

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Basic information

Entry
Database: PDB / ID: 9x3p
TitlePhage T4 sheath in post-tail-contraction state (genome-full particle)
Components
  • Tail sheath protein
  • Tail tube protein gp19
  • Tail tube terminator protein
KeywordsVIRAL PROTEIN / Bacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail / structural molecule activity
Similarity search - Function
: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain ...: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein central domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Tail tube terminator protein / Tail sheath protein / Tail tube protein gp19
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

Downloads & links

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Assembly

Deposited unit
A: Tail sheath protein
B: Tail sheath protein
C: Tail sheath protein
D: Tail sheath protein
E: Tail sheath protein
F: Tail sheath protein
G: Tail sheath protein
H: Tail sheath protein
I: Tail sheath protein
J: Tail sheath protein
K: Tail sheath protein
L: Tail sheath protein
M: Tail sheath protein
N: Tail sheath protein
O: Tail sheath protein
P: Tail sheath protein
Q: Tail sheath protein
R: Tail sheath protein
S: Tail sheath protein
T: Tail sheath protein
U: Tail sheath protein
V: Tail sheath protein
W: Tail sheath protein
b: Tail tube protein gp19
c: Tail tube protein gp19
d: Tail tube protein gp19
e: Tail tube protein gp19
f: Tail tube protein gp19
g: Tail tube protein gp19
h: Tail tube protein gp19
i: Tail tube protein gp19
j: Tail tube protein gp19
k: Tail tube protein gp19
l: Tail tube terminator protein


Theoretical massNumber of molelcules
Total (without water)1,846,52334
Polymers1,846,52334
Non-polymers00
Water00
1
A: Tail sheath protein
B: Tail sheath protein
C: Tail sheath protein
D: Tail sheath protein
E: Tail sheath protein
F: Tail sheath protein
G: Tail sheath protein
H: Tail sheath protein
I: Tail sheath protein
J: Tail sheath protein
K: Tail sheath protein
L: Tail sheath protein
M: Tail sheath protein
N: Tail sheath protein
O: Tail sheath protein
P: Tail sheath protein
Q: Tail sheath protein
R: Tail sheath protein
S: Tail sheath protein
T: Tail sheath protein
U: Tail sheath protein
V: Tail sheath protein
W: Tail sheath protein
b: Tail tube protein gp19
c: Tail tube protein gp19
d: Tail tube protein gp19
e: Tail tube protein gp19
f: Tail tube protein gp19
g: Tail tube protein gp19
h: Tail tube protein gp19
i: Tail tube protein gp19
j: Tail tube protein gp19
k: Tail tube protein gp19
l: Tail tube terminator protein
x 6


Theoretical massNumber of molelcules
Total (without water)11,079,136204
Polymers11,079,136204
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein ...
Tail sheath protein / TSP / Gene product 18 / gp18


Mass: 71391.453 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13332
#2: Protein
Tail tube protein gp19 / Gene product 19 / gp19


Mass: 18479.613 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13333
#3: Protein Tail tube terminator protein / TrP / Gene product 3 / gp3 / Tail sheath-stabilizing protein / Tail-to-head joining protein / THJP


Mass: 19723.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13331
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
32119X3P
229X3P

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2PHENIX1.19.2_4158:model refinement
13RELION3.13D reconstruction
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_d0.004131178
ELECTRON MICROSCOPYf_angle_d0.523178420
ELECTRON MICROSCOPYf_dihedral_angle_d4.62418203
ELECTRON MICROSCOPYf_chiral_restr0.04420231
ELECTRON MICROSCOPYf_plane_restr0.00423359

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