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- EMDB-3236: Electron cryo-microscopy of filamentous flexible virus PepMV (Pep... -

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Basic information

Entry
Database: EMDB / ID: EMD-3236
TitleElectron cryo-microscopy of filamentous flexible virus PepMV (Pepino Mosaic Virus)
Map dataCryoEM map of PepMV, a Potexvirus.
Sample
  • Sample: Pepino Mosaic Virus, PepMV
  • Virus: Pepino mosaic virus
KeywordsPepMV / 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 / Coat protein
Function and homology information
Biological speciesPepino mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAgirrezabala X / Mendez-Lopez E / Lasso G / Sanchez-Pina MA / Aranda MA / 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 9, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseDec 23, 2015-
UpdateAug 24, 2016-
Current statusAug 24, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fn1
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fn1
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5fn1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3236_pep...

Downloads & links

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Map

FileDownload / File: emd_3236.map.gz / Format: CCP4 / Size: 9.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of PepMV, a Potexvirus.
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.56212592 - 5.79709911
Average (Standard dev.)0.00825807 (±0.77862281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-74
Dimensions130130150
Spacing130130150
CellA: 176.8 Å / B: 176.8 Å / C: 204.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z130130150
origin x/y/z0.0000.0000.000
length x/y/z176.800176.800204.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-74
NC/NR/NS130130150
D min/max/mean-3.5625.7970.008

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Supplemental data

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Sample components

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Entire : Pepino Mosaic Virus, PepMV

EntireName: Pepino Mosaic Virus, PepMV
Components
  • Sample: Pepino Mosaic Virus, PepMV
  • Virus: Pepino mosaic virus

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Supramolecule #1000: Pepino Mosaic Virus, PepMV

SupramoleculeName: Pepino Mosaic Virus, PepMV / type: sample / ID: 1000 / Oligomeric state: Helical symmetry / Number unique components: 1
Molecular weightTheoretical: 35 MDa

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Supramolecule #1: Pepino mosaic virus

SupramoleculeName: Pepino mosaic virus / type: virus / ID: 1 / NCBI-ID: 112229 / Sci species name: Pepino mosaic virus / Sci species strain: PepMV-Sp13 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Solanum lycopersicum (tomato) / synonym: PLANTAE(HIGHER PLANTS)
Host systemOrganism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 35 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2 mg/mL
BufferpH: 8 / Details: 100 mM Tris-citric acid
GridDetails: Quantifoil R 2/2 holey carbon grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 102987 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateFeb 20, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 100 / Average electron dose: 25 e/Å2
Details: Every image is the average of 25 frames recorded by direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each partcile phase flipping
Final reconstructionApplied symmetry - Helical parameters - Δz: 3.95 Å
Applied symmetry - Helical parameters - Δ&Phi: 41.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Spring, EMAN2, CTFTILT
DetailsSpring software used

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