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 9X3R | pdb_00009x3r

Phage T4 peripheral baseplate in post-tail-contraction state (genome-full particle)

  • Classification: VIRAL PROTEIN
  • Organism(s): Escherichia phage T4
  • Mutation(s): No 

  • Deposited: 2025-10-09 Released: 2026-07-22 
  • Deposition Author(s): 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 Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9X3R

This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM Structures of Phage T4 Infection Intermediate.

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.

(2026) J Mol Biol 438: 169938-169938

  • DOI: https://doi.org/10.1016/j.jmb.2026.169938
  • Primary Citation Related Structures: 
    9UFN, 9X3O, 9X3P, 9X3Q, 9X3R, 9X3S, 9XA3

  • PubMed 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. 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.


  • Organizational Affiliation: 
    • School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China.

Macromolecule Content 

  • Total Structure Weight: 980.11 kDa 
  • Atom Count: 41,732 
  • Modeled Residue Count: 5,355 
  • Deposited Residue Count: 8,894 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate wedge protein gp8
A, B
334Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P19062 (Enterobacteria phage T4)
Explore P19062 
Go to UniProtKB:  P19062
Entity Groups
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UniProt GroupP19062
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate wedge protein gp71,032Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P19061 (Enterobacteria phage T4)
Explore P19061 
Go to UniProtKB:  P19061
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UniProt GroupP19061
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate protein gp9
D, E, F
288Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10927 (Enterobacteria phage T4)
Explore P10927 
Go to UniProtKB:  P10927
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UniProt GroupP10927
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate wedge protein gp10
G, H, I
602Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10928 (Enterobacteria phage T4)
Explore P10928 
Go to UniProtKB:  P10928
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UniProt GroupP10928
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate wedge protein gp11
J, K, L
219Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10929 (Enterobacteria phage T4)
Explore P10929 
Go to UniProtKB:  P10929
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UniProt GroupP10929
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Long-tail fiber proximal subunit
M, N, O
1,289Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P18771 (Enterobacteria phage T4)
Explore P18771 
Go to UniProtKB:  P18771
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UniProt GroupP18771
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371285
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI175340
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDP1DA060580
National Science Foundation (NSF, United States)United StatesMCB-0923873
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110243
National Institutes of Health/Office of the DirectorUnited States1S10OD023603-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references