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- PDB-6jja: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jja | ||||||||||||||||||||||||
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Title | Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP | ||||||||||||||||||||||||
![]() | Nucleocapsid protein CP17 | ||||||||||||||||||||||||
![]() | VIRUS / Giant freshwater prawn Macrobrachium rosenbergii / T=1 icosahedral particle / Single-stranded RNA satellite virus / Canonical jelly-roll beta-barrel fold / VIRUS LIKE PARTICLE | ||||||||||||||||||||||||
Function / homology | viral nucleocapsid / Nucleocapsid protein CP17![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||||||||||||||||||||
![]() | Chang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP Authors: Chang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y. | ||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.1 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.2 KB | Display | ![]() |
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Full document | ![]() | 922.7 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9705MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 19142.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Viruses / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 1.062 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() Strain: Macrobrachium rosenbergii extra small virus (Taiwan strain) | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Natural host | Organism: Macrobrachium rosenbergii | ||||||||||||||||||||
Virus shell | Name: capsid protein / Diameter: 188 nm / Triangulation number (T number): 1 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Calibrated defocus min: 510 nm / Calibrated defocus max: 3030 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5 sec. / Electron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 998 |
Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 10755 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10755 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient |