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- PDB-5a7a: Novel inter-subunit contacts in Barley Stripe Mosaic Virus reveal... -

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Basic information

Entry
Database: PDB / ID: 5a7a
TitleNovel inter-subunit contacts in Barley Stripe Mosaic Virus revealed by cryo-EM
Components
  • BARLEY STRIPE MOSAIC VIRUS NARROW
  • RNA
KeywordsVIRUS / BSMV / 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 / RNA / Capsid protein
Function and homology information
Biological speciesBARLEY STRIPE MOSAIC VIRUS
TOBACCO MOSAIC VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsClare, D.K. / Pechnikova, E. / Skurat, E. / Makarov, V. / Sokolova, O.S. / Solovyev, A.G. / V Orlova, E.
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 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
A: BARLEY STRIPE MOSAIC VIRUS NARROW
R: RNA


Theoretical massNumber of molelcules
Total (without water)23,5142
Polymers23,5142
Non-polymers00
Water0
1
A: BARLEY STRIPE MOSAIC VIRUS NARROW
R: RNA
x 106


Theoretical massNumber of molelcules
Total (without water)2,492,472212
Polymers2,492,472212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
helical symmetry operation105
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 106 / Num. of operations: 106 / Rise per n subunits: 131.2 Å / Rotation per n subunits: 1800 °)

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Components

#1: Protein BARLEY STRIPE MOSAIC VIRUS NARROW


Mass: 22555.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ONLY CONTAINS RESIDUES 3-131 AND 148-193 IN STRUCTURE
Source: (gene. exp.) BARLEY STRIPE MOSAIC VIRUS / Strain: ND18
Description: PURIFIED FROM NICOTIANA BENTHAMIANA INFECTED PLANTS
Production host: AGROBACTERIUM TUMEFACIENS (bacteria) / Strain (production host): GV3101 / References: UniProt: P04866
#2: RNA chain RNA /


Mass: 958.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOBACCO MOSAIC VIRUS / Production host: AGROBACTERIUM TUMEFACIENS (bacteria) / Strain (production host): GV3101
Sequence detailsONLY CONTAINS RESIDUES 3-131 AND 148-193 IN STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CHIMERIC BARLEY STRIPE MOSAIC VIRUS NARROW VIRION / Type: VIRUS
Buffer solutionName: 50MM TRIS-HCL, 50MM KCL, 10MM MGCL2 / pH: 7.5 / Details: 50MM TRIS-HCL, 50MM KCL, 10MM MGCL2
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 40, TEMPERATURE- 100, INSTRUMENT- HOMEMADE PLUNGER, METHOD- 3.5UL OF SAMPLE WAS ADDED TO CONTINUOUS CARBON COATED OR C-FLAT GRIDS, BLOTTED FOR 2 ...Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 40, TEMPERATURE- 100, 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 imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jun 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 150000 X / Calibrated magnification: 150000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2.3 mm
Specimen holderTemperature: 90 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 297

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2IMAGIC3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPED EACH PARTICLE
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 4.1 Å / Num. of particles: 3007 / Nominal pixel size: 1 Å / Actual pixel size: 1 Å / Magnification calibration: LAYER LINES / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY USING CHIMERA, FOLLOWED BY FLEXIBLE FITTING IN FLEX-EM AND COOT. THEN REALSPACE REFINEMENT IN PHENIX FOLLOWED BY MANUAL ADJUSTMENT IN COOT (INTERATIVE) REFINEMENT PROTOCOL--CRYO-EM
RefinementHighest resolution: 4.1 Å
Refinement stepCycle: LAST / Highest resolution: 4.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 67 0 0 1499

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