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- EMDB-2109: HRV2 full 135S particle -

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Basic information

Database: EMDB / ID: 2109
TitleHRV2 full 135S particle
Map dataReconstruction of HRV2 full 135S particle
SampleHRV2 135S full particle:
SourceHuman rhinovirus 2 (Common cold virus)
Methodsingle particle reconstruction / cryo EM / 8.8 Å resolution
AuthorsPickl-Herk A / Luque D / Trus BL / Verdaguer N / Blaas D / Caston JR
CitationJournal: 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
DateDeposition: May 27, 2012 / Header (metadata) release: Oct 3, 2012 / Map release: Aug 14, 2013 / Last update: Mar 26, 2014

Structure visualization

  • Colored surface
  • Surface level: 1.53
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.53
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_2109.map.gz (map file in CCP4 format, 56747 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
244 pix
1.89 Å/pix.
= 461.16 Å
244 pix
1.89 Å/pix.
= 461.16 Å
244 pix
1.89 Å/pix.
= 461.16 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Contour Level:1.53 (by author), 1.53 (movie #1):
Minimum - Maximum-3.96740961 - 4.60710478
Average (Standard dev.)0.05608261 (0.59235024)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 461.16 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z244244244
origin x/y/z0.0000.0000.000
length x/y/z461.160461.160461.160
start NX/NY/NZ-32-32-32
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-3.9674.6070.056

Supplemental data

Sample components

Entire HRV2 135S full particle

EntireName: HRV2 135S full particle / Number of components: 1 / Oligomeric State: icosahedral
MassTheoretical: 5.8 MDa

Component #1: virus, Human rhinovirus 2

VirusName: Human rhinovirus 2 / a.k.a: Common cold virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
SpeciesSpecies: Human rhinovirus 2 (Common cold virus)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 50 mM sodium borate / pH: 7.4
Support filmR 1.2/1.3 Quantifoil grids
VitrificationInstrument: 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

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Aug 1, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 71949 X (nominal), 79372 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3500 nm
Specimen HolderHolder: Eucentric / Model: PHILIPS ROTATION HOLDER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 186 / Sampling size: 15 microns / Bit depth: 32

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 15170 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay correction / Resolution: 8.8 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: 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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