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- PDB-5fn1: Electron cryo-microscopy of filamentous flexible virus PepMV (Pep... -

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Basic information

Entry
Database: PDB / ID: 5fn1
TitleElectron cryo-microscopy of filamentous flexible virus PepMV (Pepino Mosaic Virus)
Components
  • 5'-R(*UP*UP*UP*UP*UP)-3'
  • COAT PROTEIN
KeywordsVIRUS / PEPMV / FILAMENTOUS PLANT VIRUS / POTEXVIRUS / HELICAL SYMMETRY
Function / homologyPotexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / viral capsid / structural molecule activity / RNA / Coat protein
Function and homology information
Biological speciesPEPINO MOSAIC VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAgirrezabala, X. / Mendez-Lopez, E. / Lasso, G. / Sanchez-Pina, M.A. / Aranda, M.A. / Valle, M.
CitationJournal: Elife / Year: 2015
Title: The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses.
Authors: Xabier Agirrezabala / Eduardo Méndez-López / Gorka Lasso / M Amelia Sánchez-Pina / Miguel Aranda / Mikel Valle /
Abstract: Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We ...Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies - a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses.
History
DepositionNov 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3236
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  • Superimposition on EM map
  • EMDB-3236
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-3236
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: COAT PROTEIN
B: 5'-R(*UP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)26,6322
Polymers26,6322
Non-polymers00
Water0
1
A: COAT PROTEIN
B: 5'-R(*UP*UP*UP*UP*UP)-3'
x 18


Theoretical massNumber of molelcules
Total (without water)479,38036
Polymers479,38036
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation18
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 18 / Rise per n subunits: 3.95 Å / Rotation per n subunits: -41.1 °)

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Components

#1: Protein COAT PROTEIN / PEPINO MOSAIC VIRUS COAT PROTEIN


Mass: 25146.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PEPINO MOSAIC VIRUS / Strain: PEPMV-SP13 / References: UniProt: Q71FK2
#2: RNA chain 5'-R(*UP*UP*UP*UP*UP)-3' / PEPINO MOSAIC VIRUS SSRNA MODEL


Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PEPINO MOSAIC VIRUS / Strain: PEPMV-SP13

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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: Pepino Mosaic Virus, PepMV / Type: VIRUS
Buffer solutionName: 100 MM TRIS-CITRIC ACID / pH: 8 / Details: 100 MM TRIS-CITRIC ACID
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK II,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 20, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 102987 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 100

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Processing

EM software
IDNameVersionCategory
1CTFTILTCTF correction
2EMAN23D reconstruction
3SPRING3D reconstruction
CTF correctionDetails: EACH PARTICLE PHASE FLIPPING
3D reconstructionResolution: 3.9 Å / Actual pixel size: 1.36 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3236. (DEPOSITION ID: 14021).
Symmetry type: HELICAL
RefinementHighest resolution: 3.9 Å
Refinement stepCycle: LAST / Highest resolution: 3.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 100 0 0 1735

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