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Yorodumi- PDB-8ucr: PhiCb5 maturation protein with Caulobacter crescentus bNY30a pili -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ucr | ||||||
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Title | PhiCb5 maturation protein with Caulobacter crescentus bNY30a pili | ||||||
Components |
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Keywords | RECOMBINATION / RNA phage / protein fibril | ||||||
Function / homology | Flp/Fap pilin component / Flp/Fap pilin component / Assembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / membrane / Flp family type IVb pilin / Maturation protein Function and homology information | ||||||
Biological species | Caulobacter phage phiCb5 (virus) Caulobacter vibrioides (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.45 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 | 8ucr.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ucr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ucr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/8ucr ftp://data.pdbj.org/pub/pdb/validation_reports/uc/8ucr | HTTPS FTP |
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-Related structure data
Related structure data | 42136MC 8u2bC 8uejC 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: 40725.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter phage phiCb5 (virus) / References: UniProt: D7RIC1 |
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#2: Protein/peptide | Mass: 4379.140 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides (bacteria) / References: UniProt: A0A290MFS9 |
-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 pilus and phiCb5 maturation protein / Type: COMPLEX Details: A complex of Caulobacter crescentus pilus and ssRNA phage phiCb5 maturation protein in buffer Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.21 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Caulobacter vibrioides (bacteria) | |||||||||||||||
Buffer solution | pH: 7.5 / Details: 20mM tris, 2mM MgCl2 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
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: 40 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: 6.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56330 / Symmetry type: POINT |