|Entry||Database: EMDB / ID: 2109|
|Title||HRV2 full 135S particle|
|Map data||Reconstruction of HRV2 full 135S particle|
|Sample||HRV2 135S full particle:|
|Source||Human rhinovirus 2 (Common cold virus)|
|Method||single particle reconstruction / cryo EM / 8.8 Å resolution|
|Authors||Pickl-Herk A / Luque D / Trus BL / Verdaguer N / Blaas D / Caston JR|
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013|
Title: Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle.
Authors: Angela Pickl-Herk / Daniel Luque / Laia Vives-Adrián / Jordi Querol-Audí / Damià Garriga / Benes L Trus / Nuria Verdaguer / Dieter Blaas / José R Castón
|Date||Deposition: May 27, 2012 / Header (metadata) release: Oct 3, 2012 / Map release: Aug 14, 2013 / Last update: Mar 26, 2014|
|Structure viewer||EM map: |
Downloads & links
|File||emd_2109.map.gz (map file in CCP4 format, 56747 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.89 Å|
CCP4 map header:
-Entire HRV2 135S full particle
|Entire||Name: HRV2 135S full particle / Number of components: 1 / Oligomeric State: icosahedral|
|Mass||Theoretical: 5.8 MDa|
-Component #1: virus, Human rhinovirus 2
|Virus||Name: Human rhinovirus 2 / a.k.a: Common cold virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE|
|Species||Species: Human rhinovirus 2 (Common cold virus)|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 50 mM sodium borate / pH: 7.4|
|Support film||R 1.2/1.3 Quantifoil grids|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 99 K / Humidity: 80 %|
Method: Using a Leica EM Grid Plunger, sample was applied per grid in a humidified chamber, left for 30 s, blotted for 0.8 s and plunge-frozen
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Aug 1, 2010|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 71949 X (nominal), 79372 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3500 nm|
|Specimen Holder||Holder: Eucentric / Model: PHILIPS ROTATION HOLDER|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 186 / Sampling size: 15 microns / Bit depth: 32|
|Processing||Method: single particle reconstruction / Number of projections: 15170 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay correction / Resolution: 8.8 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: URO / Refinement protocol: rigid body / Target criteria: CC / Refinement space: RECIPROCAL|
Details: Protocol: Rigid body. The asymmetric unit was initially treated as a single rigid body and then refined, treating each subunit as an independent rigid body
Input PDB model: 3TN9
Chain ID: 1, 2, 3
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