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- PDB-8vhx: Cryo-EM of neck of bacteriophage Chi -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8vhx
TitleCryo-EM of neck of bacteriophage Chi
Components
  • Neck 1
  • Neck 2
  • Portal
  • Tail Tube
  • Tail terminator
KeywordsVIRUS / Flagellotropic bacteriophage / Siphophage / Neck
Function / homology
Function and homology information


viral portal complex / virion assembly / viral life cycle / symbiont entry into host cell / structural molecule activity / DNA binding
Similarity search - Function
Head-to-tail joining protein W / Head-to-tail joining protein W superfamily / gpW / Phage portal protein, lambda family / Phage portal protein, lambda family / 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. / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold
Similarity search - Domain/homology
Transposase / Uncharacterized protein / Portal protein / Uncharacterized protein / Major tail protein
Similarity search - Component
Biological speciesChivirus chi
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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 2, 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: Neck 1
B: Neck 1
C: Tail terminator
D: Portal
E: Portal
F: Neck 2
G: Tail Tube
H: Tail Tube


Theoretical massNumber of molelcules
Total (without water)256,4848
Polymers256,4848
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 Neck 1


Mass: 9431.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NTK8
#2: Protein Tail terminator


Mass: 18804.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NT01
#3: Protein Portal


Mass: 62333.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NUF0
#4: Protein Neck 2


Mass: 13399.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NUF1
#5: 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

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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: Neck region 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: 1.15.2_3472: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17766 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0132097
ELECTRON MICROSCOPYf_angle_d0.68657825
ELECTRON MICROSCOPYf_dihedral_angle_d19.6612862
ELECTRON MICROSCOPYf_chiral_restr0.0512435
ELECTRON MICROSCOPYf_plane_restr0.0034889

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