8VHX | pdb_00008vhx

Cryo-EM of neck of bacteriophage Chi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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

  • 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.

Macromolecule Content 

  • Total Structure Weight: 256.48 kDa 
  • Atom Count: 16,055 
  • Modeled Residue Count: 2,060 
  • Deposited Residue Count: 2,338 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neck 1
A, B
84Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NTK8 (Chivirus chi)
Explore M9NTK8 
Go to UniProtKB:  M9NTK8
Entity Groups
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UniProt GroupM9NTK8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail terminator167Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NT01 (Chivirus chi)
Explore M9NT01 
Go to UniProtKB:  M9NT01
Entity Groups
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UniProt GroupM9NT01
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Portal
D, E
560Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NUF0 (Chivirus chi)
Explore M9NUF0 
Go to UniProtKB:  M9NUF0
Entity Groups
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UniProt GroupM9NUF0
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Neck 2121Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NUF1 (Chivirus chi)
Explore M9NUF1 
Go to UniProtKB:  M9NUF1
Entity Groups
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UniProt GroupM9NUF1
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail Tube
G, H
381Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NUS9 (Chivirus chi)
Explore M9NUS9 
Go to UniProtKB:  M9NUS9
Entity Groups
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UniProt GroupM9NUS9
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15.2_3472:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510

Revision History  (Full details and data files)

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