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- EMDB-2108: HRV2 empty 135S particle -

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Basic information

Entry
Database: EMDB / ID: EMD-2108
TitleHRV2 empty 135S particle
Map dataReconstruction of HRV2 135S empty particle
Sample
  • Sample: HRV2 135S empty particle
  • Virus: Human rhinovirus 2
Biological speciesHuman rhinovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
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 /
Abstract: During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the ...During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress.
History
DepositionMay 27, 2012-
Header (metadata) releaseOct 3, 2012-
Map releaseAug 14, 2013-
UpdateMar 26, 2014-
Current statusMar 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.37
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2108.png

Downloads & links

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Map

FileDownload / File: emd_2108.map.gz / Format: CCP4 / Size: 54.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HRV2 135S empty particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 244 pix.
= 461.16 Å		1.89 Å/pix.
x 244 pix.
= 461.16 Å		1.89 Å/pix.
x 244 pix.
= 461.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.37 / Movie #1: 1.37
Minimum - Maximum-2.99722457 - 4.07371521
Average (Standard dev.)0.06360843 (±0.52530158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions244244244
Spacing244244244
CellA=B=C: 461.16 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS244244244
D min/max/mean-2.9974.0740.064

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Supplemental data

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Sample components

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Entire : HRV2 135S empty particle

EntireName: HRV2 135S empty particle
Components
  • Sample: HRV2 135S empty particle
  • Virus: Human rhinovirus 2

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Supramolecule #1000: HRV2 135S empty particle

SupramoleculeName: HRV2 135S empty particle / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightTheoretical: 5.8 MDa

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Supramolecule #1: Human rhinovirus 2

SupramoleculeName: Human rhinovirus 2 / type: virus / ID: 1 / Name.synonym: Common cold virus / NCBI-ID: 12130 / Sci species name: Human rhinovirus 2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: Common cold virus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 316 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 50 mM sodium borate
GridDetails: R 1.2/1.3 Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 99 K / Instrument: LEICA EM GP
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

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Electron microscopy

MicroscopeFEI TECNAI F30
DateAug 1, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 186 / Average electron dose: 20 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79372 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.00 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 71949
Sample stageSpecimen holder: Eucentric / Specimen holder model: PHILIPS ROTATION HOLDER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping & amplitude decay correction
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 2976

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Atomic model buiding 1

Initial modelPDB ID:

3tn9


Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 2 / Chain - #2 - Chain ID: 3
SoftwareName: URO
DetailsProtocol: Rigid body. The asymmetric unit was initially treated as a single rigid body and then refined, treating each subunit as an independent rigid body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: CC

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