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- EMDB-9705: 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-9705 | |||||||||
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Title | Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) VLP | |||||||||
![]() | The cryo-EM map of XSV-VLP | |||||||||
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Function / homology | viral nucleocapsid / Nucleocapsid protein CP17![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Wang CH / Lin HH / Wu YY / Chang WH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii extra small virus (XSV) 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 | ![]() | 117.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.4 KB 14.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.1 KB | Display | ![]() |
Images | ![]() | 318.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
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Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jjaMC 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 | The cryo-EM map of XSV-VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 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: 1.146 MDa |
Virus shell | Shell ID: 1 / Name: nucleocapsid protein CP17 / Diameter: 188.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein of giant freshwater prawn Macrobrachium rosenbergi...
Macromolecule | Name: Capsid protein of giant freshwater prawn Macrobrachium rosenbergii extra small virus type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNKRINNNRR TMRSRRGRGR TMGSNLIPYA NSPVPIPYTP PVTPVTVIGN PRKTTWIDID LSSEESGIYT LTVGSYRNRI TKLGPSKPNF IIEKVAAYAA PGDYKVVLND FKTGIQVVDE GSYAHRAAAG ILYPPAAQMF YGISATGTLN TITTTAKDPV PVVRALVTYW DSEQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 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: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||
Details | The XSV-VLPs was purified by 10-25% sucrose density gradient |
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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: 998 / Average exposure time: 20.0 sec. / Average electron dose: 100.0 e/Å2 Details: Images were collected in movie-mode with 65 frames within 5 second |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.03 µm / Calibrated defocus min: 0.51 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 |