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Yorodumi- PDB-7yjl: Melbournevirus major capsid protein built from 4.4A reconstruction -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yjl | |||||||||||||||
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Title | Melbournevirus major capsid protein built from 4.4A reconstruction | |||||||||||||||
Components | Major capsid protein | |||||||||||||||
Keywords | VIRAL PROTEIN / MCP / Melbournevirus / giant virus / major capsid protein | |||||||||||||||
Function / homology | Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / Major capsid protein Function and homology information | |||||||||||||||
Biological species | Melbournevirus | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å | |||||||||||||||
Authors | Burton-Smith, R.N. / Okamoto, K. / Murata, K. | |||||||||||||||
Funding support | Japan, Sweden, 4items
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Citation | Journal: To Be Published Title: The 4.4A structure of the giant Melbournevirus virion belonging to the Marseilleviridae family Authors: Burton-Smith, R.N. / Reddy, H.K.N. / Svenda, M. / Abergel, C. / Okamoto, K. / Murata, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yjl.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yjl.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 7yjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/7yjl ftp://data.pdbj.org/pub/pdb/validation_reports/yj/7yjl | HTTPS FTP |
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-Related structure data
Related structure data | 31529MC 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: 50896.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Melbournevirus / References: UniProt: A0A097I267 |
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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: Melbournevirus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Melbournevirus |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
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: 3000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 26.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187440 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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