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- EMDB-9205: Red Clover Necrotic Mosaic Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-9205
TitleRed Clover Necrotic Mosaic Virus
Map dataRed clover necrotic mosaic virus
Sample
  • Virus: Red clover necrotic mosaic virus
    • Protein or peptide: Capsid proteinCapsid
  • Ligand: CALCIUM IONCalcium
KeywordsRCNMV / virus
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesRed clover necrotic mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSherman MB / Smith TJ
CitationJournal: J Virol / Year: 2020
Title: Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes.
Authors: Michael B Sherman / Richard Guenther / Ron Reade / D'Ann Rochon / Tim Sit / Thomas J Smith /
Abstract: Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded ...Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of ∼340 Å. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding). Between the R domain and S domain is the "arm" region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus ) and red clover necrotic mosaic virus (RCNMV; genus ) were determined to resolutions of 3.2 Å and 2.9 Å, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the β-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit β-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell. Members of the family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the "arm," seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.
History
DepositionOct 14, 2018-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 250
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 250
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mrm
  • Surface level: 250
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mrm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9205.png

Downloads & links

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Map

FileDownload / File: emd_9205.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRed clover necrotic mosaic virus
Voxel sizeX=Y=Z: 1.0556 Å
Density
Contour LevelBy EMDB: 250.0 / Movie #1: 250
Minimum - Maximum-689.855699999999956 - 1112.650100000000066
Average (Standard dev.)0.010013332 (±70.970780000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 540.4672 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0555996093751.0555996093751.055599609375
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z540.467540.467540.467
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-689.8561112.6500.010

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Supplemental data

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Sample components

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Entire : Red clover necrotic mosaic virus

EntireName: Red clover necrotic mosaic virus
Components
  • Virus: Red clover necrotic mosaic virus
    • Protein or peptide: Capsid proteinCapsid
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Red clover necrotic mosaic virus

SupramoleculeName: Red clover necrotic mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 12267 / Sci species name: Red clover necrotic mosaic virus / Virus type: VIRION / Virus isolate: STRAIN / 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: Red clover necrotic mosaic virus
Molecular weightTheoretical: 36.617473 KDa
SequenceString: MSSKAPKKSK QRSQPRNRTP NTSVKTVAIP FAKTQIIKTV NPPPKPARGI LHTQLVMSVV GSVQMRTNNG KSNQRFRLNP SNPALFPTL AYEAANYDMY RLKKLTLRYV PLVTVQNSGR VAMIWDPDSQ DSAPQSRQEI SAYSRSVSTA VYEKCSLTIP A DNQWRFVA ...String:
MSSKAPKKSK QRSQPRNRTP NTSVKTVAIP FAKTQIIKTV NPPPKPARGI LHTQLVMSVV GSVQMRTNNG KSNQRFRLNP SNPALFPTL AYEAANYDMY RLKKLTLRYV PLVTVQNSGR VAMIWDPDSQ DSAPQSRQEI SAYSRSVSTA VYEKCSLTIP A DNQWRFVA DNTTVDRKLV DFGQLLFVTH SGSDGIETGD IFLDCEVEFK GPQPTASIVQ KTVIDLGGTL TSFEGPSYLM PP DAFITSS SFGLFVDVAG TYLLTLVVTC STTGSVTVGG NSTLVGDGRA AYGSSNYIAS IVFTSSGVLS TTPSVQFSGS SGV SRVQMN ICRCKQGNTF ILG

UniProtKB: Capsid protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1236

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