+Open data
-Basic information
Entry | Database: PDB / ID: 8vja | ||||||
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Title | Cryo-EM of tail of bacteriophage Chi | ||||||
Components | Tail Tube | ||||||
Keywords | VIRUS / Flagellotropic bacteriophage / Siphophage / Tail | ||||||
Function / homology | 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 / Major tail protein Function and homology information | ||||||
Biological species | Chivirus chi | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Sonani, R.R. / Esteves, N.C. / Scharf, B.E. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vja.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vja.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vja_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8vja_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8vja_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 8vja_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/8vja ftp://data.pdbj.org/pub/pdb/validation_reports/vj/8vja | HTTPS FTP |
-Related structure data
Related structure data | 43278MC 8vhxC 8vjhC 8vjiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 40375.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chivirus chi / References: UniProt: M9NUS9 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Chivirus chi / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Chivirus chi |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Tail of bacteriophage Chi |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.15.2_3472: / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Helical symmerty | Angular rotation/subunit: -40.83 ° / Axial rise/subunit: 40.86 Å / Axial symmetry: C6 |
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83657 / Symmetry type: HELICAL |