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- EMDB-9707: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9707 | |||||||||
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Title | Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP | |||||||||
![]() | Cryo-EM structure of MrNV full VLP | |||||||||
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Function / homology | Viral coat protein subunit / Capsid protein alpha![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Wang CH / Lin HH / Wu YY / Chang WH | |||||||||
![]() | ![]() Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP Authors: Wang CH / Lin HH / Wu YY / Chang WH | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 314.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 362.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jjdMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of MrNV full VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.026 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Viruses
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Viruses
Supramolecule | Name: Viruses / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10239 / Sci species name: Viruses / Sci species strain: Taiwan / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Host system | Organism: ![]() |
Molecular weight | Theoretical: 7.452 MDa |
Virus shell | Shell ID: 1 / Name: Capsid protein [Macrobrachium rosenbergii nodavirus] / Diameter: 400.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Capsid protein of giant freshwater prawn Macrobrachium rosenbergi...
Macromolecule | Name: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARGKQNSNQ IQNNSNANGK RRKRNRRNRN PQTVPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLIDSKSRI LVKQPISASS FLGTRISGLS QFWERYRWHK AAVRYVPAVP NTLACQLIGY IDTDPLDDPN VILDVDQLLR QATSQVGARQ ...String: MARGKQNSNQ IQNNSNANGK RRKRNRRNRN PQTVPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLIDSKSRI LVKQPISASS FLGTRISGLS QFWERYRWHK AAVRYVPAVP NTLACQLIGY IDTDPLDDPN VILDVDQLLR QATSQVGARQ WNFSDTTTIP LIVRRDDQLY YTGQDKENVR FSQQGVFYLL QVTTLLNISG EAITNDLISG SLYLDWVCGF SMPQINPSPV EVSQLTYNAD TIGNWVPPTE LKQTYTQDIT GLKPNSKFII IPYMDRVSSE VLQKCTITCN EVDAVGSISY SDTSAIKCDG YILFQANSIG EATFTLVTDY QGAVDPKPYQ YRIIRAIVGN N |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | ||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 270 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 93.0 K / Max: 103.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1353 / Average electron dose: 37.0 e/Å2 Details: Images were collected in movie-mode with 30 frames within 3 second |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.37 µm / Calibrated defocus min: 0.33 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |