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- EMDB-21260: icosahedral symmetry reconstruction of brome mosaic virus (RNA 3+4) -

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Basic information

Entry
Database: EMDB / ID: EMD-21260
Titleicosahedral symmetry reconstruction of brome mosaic virus (RNA 3+4)
Map data
Sample
  • Virus: Brome mosaic virus
    • Protein or peptide: Capsid protein
KeywordsBrome mosaic virus (RNA 3 and 4) / VIRUS
Function / homologyBromovirus coat protein / Bromovirus coat protein / T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesBrome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBeren C / Cui YX
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Genome organization and interaction with capsid protein in a multipartite RNA virus.
Authors: Christian Beren / Yanxiang Cui / Antara Chakravarty / Xue Yang / A L N Rao / Charles M Knobler / Z Hong Zhou / William M Gelbart /
Abstract: We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a ...We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes.
History
DepositionJan 30, 2020-
Header (metadata) releaseMay 20, 2020-
Map releaseMay 20, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6voc
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6voc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21260.png

Downloads & links

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Map

FileDownload / File: emd_21260.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0340241 - 0.107812375
Average (Standard dev.)0.0025432145 (±0.009947867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-175-175-175
Dimensions352352352
Spacing352352352
CellA=B=C: 376.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z376.640376.640376.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-175-175-175
NC/NR/NS352352352
D min/max/mean-0.0340.1080.003

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Supplemental data

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Sample components

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Entire : Brome mosaic virus

EntireName: Brome mosaic virus
Components
  • Virus: Brome mosaic virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Brome mosaic virus

SupramoleculeName: Brome mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12302 / Sci species name: Brome mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Brome mosaic virus
Molecular weightTheoretical: 20.411525 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString:
MSTSGTGKMT RAQRRAAARR NRWTARVQPV IVEPLAAGQG KAIKAIAGYS ISKWEASSDA ITAKATNAMS ITLPHELSSE KNKELKVGR VLLWLGLLPS VAGRIKACVA EKQAQAEAAF QVALAVADSS KEVVAAMYTD AFRGATLGDL LNLQIYLYAS E AVPAKAVV VHLEVEHVRP TFDDFFTPVY R

UniProtKB: Capsid protein

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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: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsChromatic aberration corrector: none / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 30.0 µm / Calibrated defocus min: 8.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: a Gaussian ball
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70470
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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