+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6935 | |||||||||
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Title | Cryo-EM structure of PCV3 VLP | |||||||||
Map data | Cryo-EM structure of PCV3 VLP | |||||||||
Sample |
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Function / homology | Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / viral capsid / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / Cap Function and homology information | |||||||||
Biological species | Porcine circovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 Å | |||||||||
Authors | Mo X / Yuan AY | |||||||||
Citation | Journal: to be published Title: Cryo-EM Structure of Virus-like-particle of Porcine Circovirus type 3 reveals an T=1 symmetry icosahedral particle Authors: Mo X / Yuan AY | |||||||||
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_6935.map.gz | 25.9 MB | EMDB map data format | |
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Header (meta data) | emd-6935-v30.xml emd-6935.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6935_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_6935.png | 154 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6935 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6935 | HTTPS FTP |
-Validation report
Summary document | emd_6935_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_6935_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_6935_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6935 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6935 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6935.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of PCV3 VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.69 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 : Porcine circovirus
Entire | Name: Porcine circovirus |
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Components |
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-Supramolecule #1: Porcine circovirus
Supramolecule | Name: Porcine circovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Porcine circovirus 3 capsid protein / NCBI-ID: 46221 / Sci species name: Porcine circovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host system | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) |
Molecular weight | Experimental: 1.7 MDa |
-Macromolecule #1: PCV3 capsid protein
Macromolecule | Name: PCV3 capsid protein / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Porcine circovirus |
Sequence | String: MRHRAIFRRR PRPRRRRRHR RRYVRRKLFI RRPTAGTYYT KKYSTMNVIS VGTPQNNKPW HANHFITRLN EWETAISFEY YKILKMKVT LSPVISPAQQ TKTMFGHTAI DLDGAWTTNT WLQDDPYAES STRKVMTSKK KHSRYFTPKP ILAGTTSAHP G QSLFFFSR ...String: MRHRAIFRRR PRPRRRRRHR RRYVRRKLFI RRPTAGTYYT KKYSTMNVIS VGTPQNNKPW HANHFITRLN EWETAISFEY YKILKMKVT LSPVISPAQQ TKTMFGHTAI DLDGAWTTNT WLQDDPYAES STRKVMTSKK KHSRYFTPKP ILAGTTSAHP G QSLFFFSR PTPWLNTYDP TVQWGALLWS IYVPEKTGMT DFYGTKEVWI RYKSVL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7 Component:
Details: 20mM PB(pH 6.5), 500mM NaCl | |||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before pluning. | |||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 5 / Number real images: 90 / Average exposure time: 1.0 sec. / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 47000 / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 300 |
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