+Open data
-Basic information
Entry | Database: PDB / ID: 8jou | |||||||||||||||
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Title | Fiber I and fiber-tail-adaptor of phage GP4 | |||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Complex | |||||||||||||||
Function / homology | Virion-associated phage protein / Virion-associated phage protein Function and homology information | |||||||||||||||
Biological species | Ralstonia phage GP4 (virus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Liu, H. / Chen, W. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: J Mol Biol / Year: 2023 Title: Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers. Authors: Jing Zheng / Wenyuan Chen / Hao Xiao / Fan Yang / Jingdong Song / Lingpeng Cheng / Hongrong Liu / Abstract: Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two ...Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jou.cif.gz | 274.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jou.ent.gz | 227.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jou_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8jou_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8jou_validation.xml.gz | 64.5 KB | Display | |
Data in CIF | 8jou_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/8jou ftp://data.pdbj.org/pub/pdb/validation_reports/jo/8jou | HTTPS FTP |
-Related structure data
Related structure data | 36462MC 8jovC 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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Symmetry | Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic)) |
-Components
#1: Protein | Mass: 14360.909 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GU11 #2: Protein | | Mass: 10230.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) #3: Protein | Mass: 9908.155 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GU08 |
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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: Ralstonia phage GP4 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Ralstonia phage GP4 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3800 nm / Nominal defocus min: 100 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39883 / Symmetry type: POINT | ||||||||||||||||||||||||
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