8VJA | pdb_00008vja

Cryo-EM of tail of bacteriophage Chi

• PDB DOI: https://doi.org/10.2210/pdb8VJA/pdb
• EM Map EMD-43278: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Chivirus chi
• Mutation(s): No 


• Deposited: 2024-01-06 Released: 2024-10-02 
• Deposition Author(s): Sonani, R.R., Esteves, N.C., Scharf, B.E., Egelman, E.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM structure of flagellotropic bacteriophage Chi.

Sonani, R.R., Esteves, N.C., Scharf, B.E., Egelman, E.H.

(2024) Structure 32: 856-865.e3

• PubMed: 38614087 
• DOI: https://doi.org/10.1016/j.str.2024.03.011
• Primary Citation Related Structures: 
  8VHX, 8VJA, 8VJH, 8VJI


• PubMed Abstract: 
  

  The flagellotropic bacteriophage χ (Chi) infects bacteria via the flagellar filament. Despite years of study, its structural architecture remains partly characterized. Through cryo-EM, we unveil χ's nearly complete structure, encompassing capsid, neck, tail, and tail tip. While the capsid and tail resemble phage YSD1, the neck and tail tip reveal new proteins and their arrangement. The neck shows a unique conformation of the tail tube protein, forming a socket-like structure for attachment to the neck. The tail tip comprises four proteins, including distal tail protein (DTP), two baseplate hub proteins (BH1P and BH2P), and tail tip assembly protein (TAP) exhibiting minimal organization compared to other siphophages. Deviating from the consensus in other siphophages, DTP in χ forms a trimeric assembly, reducing tail symmetry from 6-fold to 3-fold at the tip. These findings illuminate the previously unexplored structural organization of χ's neck and tail tip.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA. Electronic address: [e-mail].
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 40.38 kDa 
• Atom Count: 2,113 
• Modeled Residue Count: 275 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail Tube	A	381	Chivirus chi	Mutation(s): 0
UniProt
Find proteins for M9NUS9 (Chivirus chi) Explore M9NUS9  Go to UniProtKB:  M9NUS9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.15.2_3472:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Sonani, R.R., Esteves, N.C., Scharf, B.E., Egelman, E.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM122510

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release