|Entry||Database: EMDB / ID: 3521|
|Title||Near-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy|
|Sample||African cassava mosaic virus - [West Kenya 844]|
|Source||African cassava mosaic virus - [West Kenya 844] / virus|
|Method||single particle reconstruction, at 4.2 Å resolution|
|Authors||Bottcher B / Hipp K / Grimm C / Jeske H|
|Citation||Structure, 2017, 25, 1303-1309.e3|
|Validation Report||PDB-ID: 6ek5|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 1, 2016 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Oct 11, 2017|
Downloads & links
|File||emd_3521.map.gz (map file in CCP4 format, 108001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.57 Å|
CCP4 map header:
|File||emd_3521_msk_1.map ( map file in CCP4 format, 108001 KB )|
|Projections & Slices|
|Data type||Image stored as Reals|
|Space group number||1|
-Entire African cassava mosaic virus - [West Kenya 844]
|Entire||Name: African cassava mosaic virus - [West Kenya 844] / Number of components: 2|
|Mass||Theoretical: 3.3 MDa|
-Component #1: virus, African cassava mosaic virus - [West Kenya 844]
|Virus||Name: African cassava mosaic virus - [West Kenya 844] / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 3.3 MDa|
|Species||Species: African cassava mosaic virus - [West Kenya 844] / virus|
|Source (natural)||Host Species: Manihot esculenta / plant / キャッサバ, マニホット|
-Component #2: protein, Capsid protein
|Protein||Name: Capsid protein / Recombinant expression: No|
|Mass||Theoretical: 24.094891 kDa|
|Source (engineered)||Expression System: African cassava mosaic virus (isolate West Kenyan 844) / virus|
Strain: isolate West Kenyan 844
|Sample solution||pH: 8|
|Support film||Quantifoil R1.2/1.3 + 2nm C. Glow discharged for 30-60 s with 25-28 MicroAmp (Quorum Tec Mini Sputter coater SC7620) and used within 1 hour|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
Details: Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot IV (FEI, Eindhoven, The Netherlands) at 4?C with 100% humidity and blotting from both sides for 3 s with blot force 7
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 94000 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 934|
Details: data acquisition with a cs-corrected FEI Titan Krios on a Falcon II direct detector at 300 kV. Data was acquired at a primary magnification of 94,000 (calibrated pixel size of 1.57 A) and with a total dose of 25 e/A2 in 17 frames. In total 1,108 movies were recorded of which 934 movies were used for further processing. The movie frames were averaged after motion correction and dose weightin
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