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- PDB-8vji: Cryo-EM of capsid of bacteriophage Chi -

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Basic information

Entry
Database: PDB / ID: 8vji
TitleCryo-EM of capsid of bacteriophage Chi
Components
  • Decorator protein D
  • Major capsid protein
KeywordsVIRUS / Flagellotropic bacteriophage / Siphophage / Capsid
Function / homologyHead decoration protein D / Bacteriophage lambda head decoration protein D / Major capsid protein GpE / Phage major capsid protein E / viral capsid / host cell cytoplasm / Decorator protein D / Major capsid protein
Function and homology information
Biological speciesChivirus chi
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decorator protein D
b: Decorator protein D
c: Decorator protein D
d: Decorator protein D
e: Decorator protein D
f: Decorator protein D
g: Decorator protein D


Theoretical massNumber of molelcules
Total (without water)380,52514
Polymers380,52514
Non-polymers00
Water00
1


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

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Components

#1: Protein
Major capsid protein / Major head protein


Mass: 39959.625 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NUS8
#2: Protein
Decorator protein D


Mass: 14401.047 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NSZ8

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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: all / 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: Capsid 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
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28512 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00926319
ELECTRON MICROSCOPYf_angle_d0.79235755
ELECTRON MICROSCOPYf_dihedral_angle_d7.0283596
ELECTRON MICROSCOPYf_chiral_restr0.0513876
ELECTRON MICROSCOPYf_plane_restr0.0074683

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