+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17322 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryotomogram of Prototype Foamy Virus particles, p68 Gag | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | capsid / Gag / p68 / CA domain / VIRAL PROTEIN | |||||||||
Biological species | Eastern chimpanzee simian foamy virus | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Calcraft T / Nans A / Rosenthal PB | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
Citation | Journal: To Be Published Title: In situ cryoEM structures of PFV Authors: Calcraft T / Lindemann D / Rosenthal PB | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17322.map.gz | 603.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17322-v30.xml emd-17322.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_17322.png | 216.4 KB | ||
Filedesc metadata | emd-17322.cif.gz | 4.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17322 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17322 | HTTPS FTP |
-Validation report
Summary document | emd_17322_validation.pdf.gz | 388.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_17322_full_validation.pdf.gz | 387.9 KB | Display | |
Data in XML | emd_17322_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_17322_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17322 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17322 | HTTPS FTP |
-Related structure data
Related structure data | 17309 17311 17312 17313 17314 17315 17316 17317 17318 17319 17320 17321 8ozhC 8ozjC 8ozkC 8ozlC 8ozmC 8oznC 8ozpC 8ozqC C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_17322.map.gz / Format: CCP4 / Size: 679.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 8.88 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Eastern chimpanzee simian foamy virus
Entire | Name: Eastern chimpanzee simian foamy virus |
---|---|
Components |
|
-Supramolecule #1: Eastern chimpanzee simian foamy virus
Supramolecule | Name: Eastern chimpanzee simian foamy virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2170195 / Sci species name: Eastern chimpanzee simian foamy virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: BBI Solutions / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 1.65 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION Software:
Number images used: 37 |
---|