+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4978 | |||||||||
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Title | expanded bat circovirus with DNA VLP | |||||||||
Map data | expanded bat circovirus with DNA VLP | |||||||||
Sample |
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Keywords | expanded bat circovirus with 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 / Capsid protein Function and homology information | |||||||||
Biological species | Bat circovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.85 Å | |||||||||
Authors | Forwood JK / Luque D | |||||||||
Citation | Journal: To Be Published Title: expanded bat circovirus with DNA VLP Authors: Forwood JK / Luque D / Mata CP / Das S / Raidal S | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4978.map.gz | 27.8 MB | EMDB map data format | |
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Header (meta data) | emd-4978-v30.xml emd-4978.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_4978.png | 297.5 KB | ||
Filedesc metadata | emd-4978.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4978 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4978 | HTTPS FTP |
-Validation report
Summary document | emd_4978_validation.pdf.gz | 578.7 KB | Display | EMDB validaton report |
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Full document | emd_4978_full_validation.pdf.gz | 578.3 KB | Display | |
Data in XML | emd_4978_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_4978_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4978 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4978 | HTTPS FTP |
-Related structure data
Related structure data | 6rplMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4978.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | expanded bat circovirus with DNA VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bat circovirus
Entire | Name: Bat circovirus |
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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: No |
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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: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bat circovirus |
Molecular weight | Theoretical: 27.754744 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 524 / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 171 |
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Output model | PDB-6rpl: |