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Yorodumi- EMDB-3078: Novel inter-subunit contacts in Barley Stripe Mosaic Virus reveal... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3078 | |||||||||
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Title | Novel inter-subunit contacts in Barley Stripe Mosaic Virus revealed by cryo-EM | |||||||||
Map data | Reconstruction of the narrow Capsid of wild type BSMV | |||||||||
Sample |
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Keywords | BSMV / virus / helical / cryo-EM / image processing / MSA | |||||||||
Biological species | Barley stripe mosaic virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | |||||||||
Authors | Clare DK / Pechnikova E / Skurat E / Makarov V / Sokolova OS / Solovyev AG / Orlova EV | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3078.map.gz | 63.2 MB | EMDB map data format | |
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Header (meta data) | emd-3078-v30.xml emd-3078.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3078_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_3078.jpg | 271.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3078 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3078 | HTTPS FTP |
-Validation report
Summary document | emd_3078_validation.pdf.gz | 382.6 KB | Display | EMDB validaton report |
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Full document | emd_3078_full_validation.pdf.gz | 381.7 KB | Display | |
Data in XML | emd_3078_validation.xml.gz | 11.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3078 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3078 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3078.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the narrow Capsid of wild type BSMV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : wild type Barley Stripe Mosaic Virus narrow virion
Entire | Name: wild type Barley Stripe Mosaic Virus narrow virion |
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Components |
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-Supramolecule #1000: wild type Barley Stripe Mosaic Virus narrow virion
Supramolecule | Name: wild type 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 |
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Molecular weight | Experimental: 22.5 KDa / Theoretical: 22.5 KDa |
-Supramolecule #1: Barley stripe mosaic virus
Supramolecule | Name: 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 |
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Host (natural) | Organism: Hordeum vulgare (barley) / synonym: PLANTAE(HIGHER PLANTS) |
Host system | Organism: Nicotiana benthamiana (plant) |
Molecular weight | Experimental: 22.5 KDa / Theoretical: 22.5 KDa |
Virus shell | Shell ID: 1 / Name: narrow virion / Diameter: 216 Å |
-Macromolecule #1: RNA
Macromolecule | Name: RNA / type: rna / ID: 1 / Name.synonym: RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Barley stripe mosaic virus / Strain: ND18 / synonym: BSMV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.5 / Details: 50mM Tris-HCL, 50mM KCl, 10mM MgCl2 |
Grid | Details: c-flats r2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER Method: 3.5ul of sample was added to c-flat grids, blotted for 2 seconds and then plunged in liquid ethane |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification |
Date | Sep 15, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 330 / Average electron dose: 25 e/Å2 / Details: each image was a 1 second low dose exposure / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 150000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |