+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4977 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | non-expanded bat circovirus with DNA VLP | |||||||||
Map data | Bat circovirus DNA non-expanded class (class01) | |||||||||
Sample |
| |||||||||
Keywords | non-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: 2.84 Å | |||||||||
Authors | Forwood JK / Luque D | |||||||||
Citation | Journal: To Be Published Title: non-expanded bat circovirus with DNA VLP Authors: Forwood JK / Luque D / Mata CP / Das S / Raidal S | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4977.map.gz | 28.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4977-v30.xml emd-4977.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_4977.png | 302.8 KB | ||
Filedesc metadata | emd-4977.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4977 | HTTPS FTP |
-Related structure data
Related structure data | 6rpkMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4977.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Bat circovirus DNA non-expanded class (class01) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Bat circovirus
Entire | Name: Bat circovirus |
---|---|
Components |
|
-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 |
---|---|
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 |
---|---|
Source (natural) | Organism: Bat circovirus |
Molecular weight | Theoretical: 23.749828 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RFRARYRWRR KNGITNLRLT RQVELWVPKD AANASFYVNH YTFDLDDFIP AGTQLNSSPL PFKYYRIRKV KVEFQPRLPI TSPFRGYGS TVPILDGAFV TPATGESDPI WDPYINFSGR HVIRTPAWYH KRYFTPKPLI DGNTGFFQPN NKQNALWFPN K QGQNIQWS ...String: RFRARYRWRR KNGITNLRLT RQVELWVPKD AANASFYVNH YTFDLDDFIP AGTQLNSSPL PFKYYRIRKV KVEFQPRLPI TSPFRGYGS TVPILDGAFV TPATGESDPI WDPYINFSGR HVIRTPAWYH KRYFTPKPLI DGNTGFFQPN NKQNALWFPN K QGQNIQWS GLGFAMQKGN EAYNYQVRFT LYVQFREFDL FNN UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
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 |
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 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 195079 |
---|---|
Startup model | Type of model: EMDB MAP |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Number classes: 4 / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 56911 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 97 |
---|---|
Output model | PDB-6rpk: |