- EMDB-11621: Class 4 of three-dimensional classification of single asymmetric ... -
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Basic information
Entry
Database: EMDB / ID: EMD-11621
Title
Class 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 data
Class 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 species
Rhinovirus A
Method
single particle reconstruction / cryo EM / Resolution: 2.9 Å
Journal: 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
Deposition
Aug 17, 2020
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Header (metadata) release
Sep 16, 2020
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Map release
Sep 16, 2020
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Update
Oct 14, 2020
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Current status
Oct 14, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_11621.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Class 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.
Voxel size
X=Y=Z: 0.97 Å
Density
Contour Level
By AUTHOR: 0.002 / Movie #1: 0.002
Minimum - Maximum
-0.011815332 - 0.018784637
Average (Standard dev.)
0.0000088368 (±0.00030056562)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
450
450
450
Spacing
450
450
450
Cell
A=B=C: 436.5 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
0.97
0.97
0.97
M x/y/z
450
450
450
origin x/y/z
0.000
0.000
0.000
length x/y/z
436.500
436.500
436.500
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
161
186
271
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
450
450
450
D min/max/mean
-0.012
0.019
0.000
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Supplemental data
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Sample components
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Entire : Rhinovirus A
Entire
Name: Rhinovirus A
Components
Virus: Rhinovirus A
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Supramolecule #1: Rhinovirus A
Supramolecule
Name: 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 shell
Shell ID: 1 / Diameter: 302.0 Å
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.4
Vitrification
Cryogen name: ETHANE
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Electron microscopy
Microscope
FEI POLARA 300
Electron beam
Acceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
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