+Open data
-Basic information
Entry | Database: PDB / ID: 8h89 | |||||||||||||||
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Title | Capsid of Ralstonia phage GP4 | |||||||||||||||
Components |
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Keywords | VIRUS / Ralstonia phage GP4 / Complex | |||||||||||||||
Function / homology | Protein of unknown function DUF4043 / Protein of unknown function (DUF4043) / Virion associated protein / Major capsid protein Function and homology information | |||||||||||||||
Biological species | Ralstonia phage GP4 (virus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Liu, H.R. / Chen, W.Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Viruses / Year: 2022 Title: A Capsid Structure of GP4 with a Triangulation Number T = 9. Authors: Jing Zheng / Wenyuan Chen / Hao Xiao / Fan Yang / Xiaowu Li / Jingdong Song / Lingpeng Cheng / Hongrong Liu / Abstract: GP4, a new phage, is a short-tailed phage. Few structures of phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo- ...GP4, a new phage, is a short-tailed phage. Few structures of phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between and corresponding phages. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h89.cif.gz | 755.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h89.ent.gz | 637 KB | Display | PDB format |
PDBx/mmJSON format | 8h89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h89_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
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Full document | 8h89_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 8h89_validation.xml.gz | 90.6 KB | Display | |
Data in CIF | 8h89_validation.cif.gz | 138.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/8h89 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/8h89 | HTTPS FTP |
-Related structure data
Related structure data | 34539MC 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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-Components
#1: Protein | Mass: 40819.551 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GTT3 #2: Protein | Mass: 15819.934 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GTT2 |
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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
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40792 / Symmetry type: POINT | ||||||||||||||||||||||||
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