8VJH | pdb_00008vjh

Cryo-EM of tail-tip of bacteriophage Chi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8VJH

This is version 1.0 of the entry. See complete history

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: 478.77 kDa 
  • Atom Count: 15,967 
  • Modeled Residue Count: 2,219 
  • Deposited Residue Count: 4,399 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Minor tail protein1,296Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NVD3 (Chivirus chi)
Explore M9NVD3 
Go to UniProtKB:  M9NVD3
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UniProt GroupM9NVD3
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Distal tail protein562Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NT03 (Chivirus chi)
Explore M9NT03 
Go to UniProtKB:  M9NT03
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UniProt GroupM9NT03
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate hub 1 protein, gp27C [auth D]272Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NUT0 (Chivirus chi)
Explore M9NUT0 
Go to UniProtKB:  M9NUT0
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UniProt GroupM9NUT0
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail TubeD [auth J],
E [auth K]
381Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NUS9 (Chivirus chi)
Explore M9NUS9 
Go to UniProtKB:  M9NUS9
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Tape measureF [auth Q]1,431Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NVD0 (Chivirus chi)
Explore M9NVD0 
Go to UniProtKB:  M9NVD0
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail assembly protein 1G [auth U]76Chivirus chiMutation(s): 0 
UniProt
Find proteins for M9NTL4 (Chivirus chi)
Explore M9NTL4 
Go to UniProtKB:  M9NTL4
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
H [auth D]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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