+Open data
-Basic information
Entry | Database: PDB / ID: 7xf2 | ||||||
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Title | Cry-EM structure of vp51 in white spot syndrome virus capsid | ||||||
Components | Capsid protein | ||||||
Keywords | VIRAL PROTEIN / Complex / C14 / capsid / disc | ||||||
Function / homology | viral envelope / DNA binding / Capsid protein Function and homology information | ||||||
Biological species | White spot syndrome virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.73 Å | ||||||
Authors | Shan, H. / Shen, Q.T. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: structure of vp51 in white spot syndrome virus capsid Authors: Hong, S. / Shen, Q.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xf2.cif.gz | 153.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xf2.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/7xf2 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/7xf2 | HTTPS FTP |
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-Related structure data
Related structure data | 33168MC 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: 51965.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) White spot syndrome virus / References: UniProt: K7WK08 |
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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: white spot syndrome virus / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: White spot syndrome virus |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NEGATIVE / Material: uranyl acetate |
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: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153916 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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