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- PDB-8vjh: Cryo-EM of tail-tip of bacteriophage Chi -

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Basic information

Entry
Database: PDB / ID: 8vjh
TitleCryo-EM of tail-tip of bacteriophage Chi
Components
  • Baseplate hub 1 protein, gp27
  • Distal tail protein
  • Minor tail protein
  • Tail Tube
  • Tail assembly protein 1
  • Tape measure
KeywordsVIRUS / Flagellotropic bacteriophage / Siphophage / Tail-tip
Function / homology
Function and homology information


Tape measure protein N-terminal / Tape measure protein / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Tip attachment protein J ...Tape measure protein N-terminal / Tape measure protein / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Tip attachment protein J / Putative phage tail protein / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Distal tail protein / Tail assembly protein 1 / Major tail protein / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Tape measure / Minor tail protein
Similarity search - Component
Biological speciesChivirus chi
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSonani, R.R. / Esteves, N.C. / Scharf, B.E. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Structure / Year: 2024
Title: Cryo-EM structure of flagellotropic bacteriophage Chi.
Authors: Ravi R Sonani / Nathaniel C Esteves / Birgit E Scharf / Edward H Egelman /
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 ...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.
History
DepositionJan 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor tail protein
B: Distal tail protein
D: Baseplate hub 1 protein, gp27
J: Tail Tube
K: Tail Tube
Q: Tape measure
U: Tail assembly protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,7708
Polymers478,7147
Non-polymers561
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 7 molecules ABDJKQU

#1: Protein Minor tail protein


Mass: 143342.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NVD3
#2: Protein Distal tail protein


Mass: 63032.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NT03
#3: Protein Baseplate hub 1 protein, gp27


Mass: 29348.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NUT0
#4: Protein Tail Tube


Mass: 40375.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NUS9
#5: Protein Tape measure


Mass: 153960.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NVD0
#6: Protein Tail assembly protein 1


Mass: 8278.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NTL4

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chivirus chi / Type: VIRUS / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Chivirus chi
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Tail-tip of bacteriophage Chi
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2159 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216277
ELECTRON MICROSCOPYf_angle_d0.55721977
ELECTRON MICROSCOPYf_dihedral_angle_d5.7262401
ELECTRON MICROSCOPYf_chiral_restr0.0452239
ELECTRON MICROSCOPYf_plane_restr0.0043019

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