+Open data
-Basic information
Entry | Database: PDB / ID: 8uej | ||||||
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Title | ssRNA phage PhiCb5 virion | ||||||
Components |
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Keywords | VIRUS / ssRNA phage | ||||||
Function / homology | Assembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / viral capsid / Maturation protein / Coat protein Function and homology information | ||||||
Biological species | Caulobacter phage phiCb5 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Wang, Y. / Zhang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus. Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang / Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uej.cif.gz | 3.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8uej.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8uej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/8uej ftp://data.pdbj.org/pub/pdb/validation_reports/ue/8uej | HTTPS FTP |
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-Related structure data
Related structure data | 42163MC 8u2bC 8ucrC C: citing same article (ref.) M: map data used to model this data |
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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: 13498.981 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Source: (natural) Caulobacter phage phiCb5 (virus) / References: UniProt: D7RIC2 #2: Protein | | Mass: 40725.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter phage phiCb5 (virus) / References: UniProt: D7RIC1 #3: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: A complex of phiCb5 maturation protein and phiCb5 shell Type: COMPLEX Details: A complex of phiCb5 maturation protein and phiCb5 shell Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 2.1 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Caulobacter vibrioides (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 20mM tris, 2mM MgCl2, 3mM CaCl2 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid type: C-flat-2/1 | ||||||||||||||||||||
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 FIELDBright-field microscopy / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.17.1_3660: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272204 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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