[English] 日本語
Yorodumi- PDB-6jjd: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jjd | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP | |||||||||||||||||||||||||||
Components | Capsid protein | |||||||||||||||||||||||||||
Keywords | VIRUS LIKE PARTICLE / Giant freshwater prawn Macrobrachium rosenbergii / T=3 icosahedral particle / Double-stranded RNA virus / Canonical jelly-roll beta-barrel fold | |||||||||||||||||||||||||||
Function / homology | Viral coat protein subunit / Capsid protein alpha Function and homology information | |||||||||||||||||||||||||||
Biological species | Macrobrachium rosenbergii nodavirus | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å | |||||||||||||||||||||||||||
Authors | Chang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y. | |||||||||||||||||||||||||||
Funding support | Taiwan, 8items
| |||||||||||||||||||||||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP Authors: Chang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y. | |||||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jjd.cif.gz | 214.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jjd.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 6jjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jjd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jjd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6jjd_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 6jjd_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jjd ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jjd | HTTPS FTP |
-Related structure data
Related structure data | 9707MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 41480.641 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrobrachium rosenbergii nodavirus / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15BP6 #2: Chemical | ChemComp-CA / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Viruses / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 7.452 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Viruses | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pETDuet-1 | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Natural host | Organism: Macrobrachium rosenbergii / Strain: Taiwan strain | ||||||||||||||||||||
Virus shell | Name: capsid protein / Diameter: 400 nm / Triangulation number (T number): 3 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 0.1 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 |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Calibrated defocus min: 330 nm / Calibrated defocus max: 3370 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: 3 sec. / Electron dose: 37 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1353 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8856 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8856 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient |