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- EMDB-3074: Novel inter-subunit contacts in Barley Stripe Mosaic Virus reveal... -

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Basic information

Entry
Database: EMDB / ID: EMD-3074
TitleNovel inter-subunit contacts in Barley Stripe Mosaic Virus revealed by cryo-EM
Map dataReconstruction of the narrow Capsid of BSMV
Sample
  • Sample: chimeric Barley Stripe Mosaic Virus narrow virion
  • Virus: Barley stripe mosaic virus
  • RNA: RNA
KeywordsBSMV / virus / helical / cryo-EM / image processing / MSA
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein
Function and homology information
Biological speciesTobacco mosaic virus / Barley stripe mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsClare DK / Pechnikova E / Skurat E / Makarov V / Sokolova OS / Solovyev AG / Orlova EV
CitationJournal: Structure / Year: 2015
Title: Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy.
Authors: Daniel Kofi Clare / Eugenia V Pechnikova / Eugene V Skurat / Valentin V Makarov / Olga S Sokolova / Andrey G Solovyev / Elena V Orlova /
Abstract: Barley stripe mosaic virus (BSMV, genus Hordeivirus) is a rod-shaped single-stranded RNA virus similar to viruses of the structurally characterized and well-studied genus Tobamovirus. Here we report ...Barley stripe mosaic virus (BSMV, genus Hordeivirus) is a rod-shaped single-stranded RNA virus similar to viruses of the structurally characterized and well-studied genus Tobamovirus. Here we report the first high-resolution structure of BSMV at 4.1 Å obtained by cryo-electron microscopy. We discovered that BSMV forms two types of virion that differ in the number of coat protein (CP) subunits per turn and interactions between the CP subunits. While BSMV and tobacco mosaic virus CP subunits have a similar fold and interact with RNA using conserved residues, the axial contacts between the CP of these two viral groups are considerably different. BSMV CP subunits lack substantial axial contacts and are held together by a previously unobserved lateral contact formed at the virion surface via an interacting loop, which protrudes from the CP hydrophobic core to the adjacent CP subunit. These data provide an insight into diversity in structural organization of helical viruses.
History
DepositionJul 1, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseSep 2, 2015-
UpdateOct 21, 2015-
Current statusOct 21, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 30
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5a7a
  • Surface level: 30
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5a7a
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3074.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the narrow Capsid of BSMV
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 20.0 / Movie #1: 30
Minimum - Maximum-111.187492370000001 - 169.57945251000001
Average (Standard dev.)0.24112175 (±19.142253879999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-111.187169.5790.241

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Supplemental data

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Sample components

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Entire : chimeric Barley Stripe Mosaic Virus narrow virion

EntireName: chimeric Barley Stripe Mosaic Virus narrow virion
Components
  • Sample: chimeric Barley Stripe Mosaic Virus narrow virion
  • Virus: Barley stripe mosaic virus
  • RNA: RNA

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Supramolecule #1000: chimeric Barley Stripe Mosaic Virus narrow virion

SupramoleculeName: chimeric Barley Stripe Mosaic Virus narrow virion / type: sample / ID: 1000
Details: The sample is a helical virus with 106 copies of the capsid protein per helical repeat
Oligomeric state: Helical, with 106 copies of the capsid protein per helical repeat
Number unique components: 2
Molecular weightExperimental: 22.5 KDa / Theoretical: 22.5 KDa

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Supramolecule #1: Barley stripe mosaic virus

SupramoleculeName: Barley stripe mosaic virus / type: virus / ID: 1 / Name.synonym: BSMV / Details: Has RNA bound / NCBI-ID: 12327 / Sci species name: Barley stripe mosaic virus / Sci species strain: ND18 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: BSMV
Host (natural)Organism: Hordeum vulgare (barley) / synonym: PLANTAE(HIGHER PLANTS)
Host systemOrganism: Nicotiana benthamiana (plant)
Molecular weightExperimental: 22.5 KDa / Theoretical: 22.5 KDa
Virus shellShell ID: 1 / Name: narrow virion / Diameter: 216 Å

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Macromolecule #1: RNA

MacromoleculeName: RNA / type: rna / ID: 1 / Name.synonym: RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Tobacco mosaic virus
SequenceString:
GAA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5 / Details: 50mM Tris-HCL, 50mM KCl, 10mM MgCl2
GridDetails: c-flats r2/2 or home made continuous carbon grids
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER
Method: 3.5ul of sample was added to continuous carbon coated or c-flat grids, blotted for 2 seconds and then plunged in liquid ethane

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 150000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: GATAN HELIUM
TemperatureMin: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateJun 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 297 / Average electron dose: 25 e/Å2 / Details: each image was a 1 second low dose exposure / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipped each particle
Final angle assignmentDetails: 1 degree steps from 80-100 degrees in beta and from 0-16.98 degrees in gamma
Final reconstructionApplied symmetry - Helical parameters - Δz: 1.238 Å
Applied symmetry - Helical parameters - Δ&Phi: 16.98 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: eman, Imagic, spider / Details: Final maps calculated with BPRP / Number images used: 3007
DetailsBPRP was used for reconstruction. The particles were selected using the helical option in boxer. Helical symmetry was imposed, with 106 subunits in the 5 turns forming the helical repeat.
FSC plot (resolution estimation)

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