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- PDB-9ufn: Phage T4 hub in post-tail contraction, pre-genome-release state -

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Basic information

Entry
Database: PDB / ID: 9ufn
TitlePhage T4 hub in post-tail contraction, pre-genome-release state
Components
  • Baseplate tail-tube junction protein gp48
  • Baseplate tail-tube junction protein gp54
  • Tail tube protein gp19
KeywordsVIRAL PROTEIN / Bacteriophage / Myovirus / Phage T4 / tail contraction / phage hub complex / tape-measure protein / genome release
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / viral tail assembly / structural molecule activity
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19
Similarity search - Domain/homology
Tail tube protein gp19 / Baseplate tail-tube junction protein gp48 / Baseplate tail-tube junction protein gp54
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShao, Q. / Dong, J. / Wang, A. / Li, L. / Zheng, Y. / Li, H. / Li, Y. / Zhang, Q. / Sun, L. / Fokine, A. ...Shao, Q. / Dong, J. / Wang, A. / Li, L. / Zheng, Y. / Li, H. / Li, Y. / Zhang, Q. / 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: To Be Published
Title: Near-atomic structure of a viral genome delivery machine intermediate from bacteriophage T4
Authors: Shao, Q. / Dong, J. / Wang, A. / Li, L. / Zheng, Y. / Li, H. / Li, Y. / Zhang, Q. / Sun, L. / Fokine, A. / Rao, V.B. / Tao, P. / Fang, Q.
History
DepositionApr 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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 tube protein gp19
B: Tail tube protein gp19
C: Baseplate tail-tube junction protein gp54
D: Baseplate tail-tube junction protein gp48


Theoretical massNumber of molelcules
Total (without water)111,7454
Polymers111,7454
Non-polymers00
Water00
1
A: Tail tube protein gp19
B: Tail tube protein gp19
C: Baseplate tail-tube junction protein gp54
D: Baseplate tail-tube junction protein gp48
x 6


Theoretical massNumber of molelcules
Total (without water)670,46924
Polymers670,46924
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 Tail tube protein gp19 / Gene product 19 / gp19


Mass: 18479.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13333
#2: Protein Baseplate tail-tube junction protein gp54 / Gene product 54 / gp54


Mass: 35015.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13341
#3: Protein Baseplate tail-tube junction protein gp48 / Baseplate-tube cap / Gene product 48 / gp48


Mass: 39770.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P13339
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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
110.2540SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)2276
210.2559.6GATAN K3 (6k x 4k)5090
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scans
Movie frames/imageIDImage recording-IDEntry-ID
32119UFN
229UFN

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Processing

EM software
IDNameVersionCategory
2PHENIX1.19.2_4158:model refinement
3EPUimage acquisition
4SerialEMimage acquisition
6CTFFIND4CTF correction
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 40108
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36951 / Symmetry type: POINT

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