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- EMDB-11621: Class 4 of three-dimensional classification of single asymmetric ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11621
TitleClass 4 of three-dimensional classification of single asymmetric units of RV-A89 into six classes. The class averages reveal differences at the RNA/protein interfaces.
Map dataClass 4 of three-dimensional classification of single asymmetric units of RV-A89 into six classes. The class averages reveal differences at the RNA/protein interfaces.
Sample
  • Virus: Rhinovirus A
Biological speciesRhinovirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBlaas D
Funding support Austria, 2 items
OrganizationGrant numberCountry
Austrian Science Fund31293 Austria
Austrian Science Fund27444 Austria
CitationJournal: Commun Biol / Year: 2020
Title: Individual subunits of a rhinovirus causing common cold exhibit largely different protein-RNA contact site conformations.
Authors: Dieter Blaas /
Abstract: Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA ...Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA genome. Three-D classification of single and oligomeric asymmetric units computationally excised from a 2.9 Å cryo-EM density map of rhinovirus A89, showed that VP4 and the N-terminal extension of VP1 adopt different conformations within the otherwise identical 3D-structures. Analysis of up to sixty classes of single subunits and of six classes of subunit dimers, trimers, and pentamers revealed different orientations of the amino acid residues at the interface with the RNA suggesting that local asymmetry is dictated by disparities of the interacting nucleotide sequences. The different conformations escape detection by 3-D structure determination of entire virions with the conformational heterogeneity being only indicated by low density. My results do not exclude that the RNA follows a conserved assembly mechanism, contacting most or all asymmetric units in a specific way. However, as suggested by the gradual loss of asymmetry with increasing oligomerization and the 3D-structure of entire virions reconstructed by using Euler angles selected in the classification of single subunits, RNA path and/or folding likely differ from virion to virion.
History
DepositionAug 17, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11621.png

Downloads & links

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Map

FileDownload / File: emd_11621.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass 4 of three-dimensional classification of single asymmetric units of RV-A89 into six classes. The class averages reveal differences at the RNA/protein interfaces.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 450 pix.
= 436.5 Å		0.97 Å/pix.
x 450 pix.
= 436.5 Å		0.97 Å/pix.
x 450 pix.
= 436.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002 / Movie #1: 0.002
Minimum - Maximum-0.011815332 - 0.018784637
Average (Standard dev.)0.0000088368 (±0.00030056562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 436.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.970.970.97
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z436.500436.500436.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0120.0190.000

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Supplemental data

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Sample components

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Entire : Rhinovirus A

EntireName: Rhinovirus A
Components
  • Virus: Rhinovirus A

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Supramolecule #1: Rhinovirus A

SupramoleculeName: Rhinovirus A / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 147711 / Sci species name: Rhinovirus A / Sci species strain: Rhinovirus A89 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 302.0 Å

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107054
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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