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- PDB-9x3r: Phage T4 peripheral baseplate in post-tail-contraction state (gen... -

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Basic information

Entry
Database: PDB / ID: 9x3r
TitlePhage T4 peripheral baseplate in post-tail-contraction state (genome-full particle)
Components
  • (Baseplate wedge protein ...) x 4
  • Baseplate protein gp9
  • Long-tail fiber proximal subunit
KeywordsVIRAL PROTEIN / Bacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / virus tail, fiber / viral release from host cell
Similarity search - Function
: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate wedge protein gp7 / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain ...: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate wedge protein gp7 / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / : / : / : / GP11 baseplate wedge protein / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp10 / : / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Long-tail fiber proximal subunit / Baseplate wedge protein gp7 / Baseplate wedge protein gp8
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. / 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: Baseplate wedge protein gp8
B: Baseplate wedge protein gp8
C: Baseplate wedge protein gp7
D: Baseplate protein gp9
E: Baseplate protein gp9
F: Baseplate protein gp9
G: Baseplate wedge protein gp10
H: Baseplate wedge protein gp10
I: Baseplate wedge protein gp10
J: Baseplate wedge protein gp11
K: Baseplate wedge protein gp11
L: Baseplate wedge protein gp11
M: Long-tail fiber proximal subunit
N: Long-tail fiber proximal subunit
O: Long-tail fiber proximal subunit


Theoretical massNumber of molelcules
Total (without water)980,10815
Polymers980,10815
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Baseplate wedge protein ... , 4 types, 9 molecules ABCGHIJKL

#1: Protein Baseplate wedge protein gp8 / Gene product 8 / gp8


Mass: 38041.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P19062
#2: Protein Baseplate wedge protein gp7 / Gene product 7 / gp7


Mass: 119336.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P19061
#4: Protein Baseplate wedge protein gp10 / Gene product 10 / gp10


Mass: 66281.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10928
#5: Protein Baseplate wedge protein gp11 / Gene product 11 / gp11


Mass: 23725.523 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10929

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Protein , 2 types, 6 molecules DEFMNO

#3: Protein Baseplate protein gp9 / Gene product 9 / gp9


Mass: 31024.725 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10927
#6: Protein Long-tail fiber proximal subunit / Gene product 34 / gp34


Mass: 140530.922 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P18771

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Details

Has protein modificationY

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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: #1-#5 / 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
32119X3R
229X3R

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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: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235806 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00342637
ELECTRON MICROSCOPYf_angle_d0.49358064
ELECTRON MICROSCOPYf_dihedral_angle_d4.1945780
ELECTRON MICROSCOPYf_chiral_restr0.0456523
ELECTRON MICROSCOPYf_plane_restr0.0047606

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