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 9X3O | pdb_00009x3o

Phage T4 neck 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: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9X3O

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: 564.42 kDa 
  • Atom Count: 19,671 
  • Modeled Residue Count: 2,445 
  • Deposited Residue Count: 5,116 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Portal protein
A, B
524Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P13334 (Enterobacteria phage T4)
Explore P13334 
Go to UniProtKB:  P13334
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13334
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Neck protein gp13
C, D
309Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P11110 (Enterobacteria phage T4)
Explore P11110 
Go to UniProtKB:  P11110
Entity Groups
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UniProt GroupP11110
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Neck protein gp14256Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P11111 (Enterobacteria phage T4)
Explore P11111 
Go to UniProtKB:  P11111
Entity Groups
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UniProt GroupP11111
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail completion protein gp15272Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P11112 (Enterobacteria phage T4)
Explore P11112 
Go to UniProtKB:  P11112
Entity Groups
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UniProt GroupP11112
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibritin
G, H, I, J, K
G, H, I, J, K, L
487Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Entity Groups
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UniProt GroupP10104
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19.2_4158

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