|Entry||Database: EMDB / ID: 5699|
|Title||CryoEM structure of EGFR-specific virus (derived from sindbis virus)|
|Map data||CryoEM structure of EGFR-specific virus derived from sindbis virus|
|Sample||EGFR-specific virus (derived from sindbis virus):|
|Keywords||EGFR-specific virus / sindbis virus|
|Source||synthetic construct (EGFR-specific Sindbis virus)|
|Method||single particle reconstruction / cryo EM / 12.2 Å resolution|
|Authors||Dai H / Liu Z / Jiang W / Kuhn RJ|
|Citation||Journal: J. Virol. / Year: 2013|
Title: Directed evolution of a virus exclusively utilizing human epidermal growth factor receptor as the entry receptor.
Authors: Hong-Sheng Dai / Zheng Liu / Wen Jiang / Richard J Kuhn
|Date||Deposition: Jun 25, 2013 / Header (metadata) release: Aug 28, 2013 / Map release: Jul 30, 2014 / Last update: Oct 12, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5699.map.gz (map file in CCP4 format, 132862 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3.24 Å|
CCP4 map header:
-Entire EGFR-specific virus (derived from sindbis virus)
|Entire||Name: EGFR-specific virus (derived from sindbis virus) / Details: The sample was monodisperse. / Number of components: 1 / Oligomeric State: icosahedral|
-Component #1: virus, synthetic construct
|Virus||Name: synthetic construct / a.k.a: EGFR-specific Sindbis virus / Class: VIRION|
Details: EGF domain was engrafted onto an icosahedral virus scaffold, and directed evolution was conducted to stabilize the chimeric virus.
Empty: No / Enveloped: Yes / Isolate: STRAIN
|Species||Species: synthetic construct (EGFR-specific Sindbis virus) / Strain: EGFR-specific no.1|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Shell #1||Name of element: E1 and E2-EGF / Diameter: 375.00 Å / T number(triangulation number): 4|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1.5 mg/ml / Buffer solution: 50 mM Tris, 200 mM NaCl, 1 mM EDTA / pH: 7.4|
|Support film||400 mesh copper grid with thin carbon support, glow discharged in air|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 97.15 K / Humidity: 70 % / Method: Blot for 6 seconds before plunging.|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG / Date: Oct 12, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 38000 X (nominal), 39190 X (calibrated)|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 5000 nm
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC / Temperature: 97 K ( 93.15 - 100.15 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 166 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 3.24 microns / Bit depth: 16|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2290|
|3D reconstruction||Algorithm: projection matching / Software: jspr, EMAN2, EMAN / CTF correction: each particle / Details: Final maps were calculated from 2290 particles. / Resolution: 12.2 Å|
Resolution method: FSC at 0.143 cut-off between two independently refined density maps, gold-standard
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