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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4979 | |||||||||
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Title | bat circovirus without DNA VLP | |||||||||
![]() | bat circovirus without DNA VLP | |||||||||
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![]() | bat circovirus without DNA VLP / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / Capsid protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.39 Å | |||||||||
![]() | Forwood JK / Luque D | |||||||||
![]() | ![]() Title: bat circovirus without DNA VLP Authors: Forwood JK / Luque D / Mata CP / Das S / Raidal S | |||||||||
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 | ![]() | 62.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 294.1 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 725.1 KB | Display | ![]() |
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Full document | ![]() | 724.7 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rpoMC 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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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | bat circovirus without DNA VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 : Bat circovirus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Bat circovirus
Supramolecule | Name: Bat circovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1329650 / Sci species name: Bat circovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Molecular weight | Theoretical: 1.42 MDa |
Virus shell | Shell ID: 1 / Diameter: 200.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: bat circovirus capsid protein
Macromolecule | Name: bat circovirus capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.754744 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MVYRRRRGRG RRARPMSSLG RLLYRKPWLM HPRFRARYRW RRKNGITNLR LTRQVELWVP KDAANASFYV NHYTFDLDDF IPAGTQLNS SPLPFKYYRI RKVKVEFQPR LPITSPFRGY GSTVPILDGA FVTPATGESD PIWDPYINFS GRHVIRTPAW Y HKRYFTPK ...String: MVYRRRRGRG RRARPMSSLG RLLYRKPWLM HPRFRARYRW RRKNGITNLR LTRQVELWVP KDAANASFYV NHYTFDLDDF IPAGTQLNS SPLPFKYYRI RKVKVEFQPR LPITSPFRGY GSTVPILDGA FVTPATGESD PIWDPYINFS GRHVIRTPAW Y HKRYFTPK PLIDGNTGFF QPNNKQNALW FPNKQGQNIQ WSGLGFAMQK GNEAYNYQVR FTLYVQFREF DLFNN |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1474 / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 47170 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 83 |
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Output model | ![]() PDB-6rpo: |