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- EMDB-3785: Structure of Watermelon mosaic virus potyvirus. -

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Basic information

Database: EMDB / ID: 3785
TitleStructure of Watermelon mosaic virus potyvirus.
SampleWatermelon mosaic virus
SourceWatermelon mosaic virus / virus
Map dataCryoelectron microscopy map of Watermelon mosaic virus filament. Resulting map from Relion postprocessing.
Methodhelical reconstruction, at 4 Å resolution
AuthorsZamora M / Mendez-Lopez E
CitationSci Adv, 2017, 3, eaao2182-eaao2182

Sci Adv, 2017, 3, eaao2182-eaao2182 Yorodumi Papers
Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses.
Miguel Zamora / Eduardo Méndez-López / Xabier Agirrezabala / Rebeca Cuesta / José L Lavín / M Amelia Sánchez-Pina / Miguel A Aranda / Mikel Valle

Validation ReportPDB-ID: 5odv

SummaryFull reportAbout validation report
DateDeposition: Jul 6, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Sep 27, 2017 / Last update: Oct 11, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5odv
  • Surface level: 0.021
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5odv
  • Imaged by Jmol
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_3785.map.gz (map file in CCP4 format, 48669 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
230 pix
1.1 Å/pix.
= 253. Å
230 pix
1.1 Å/pix.
= 253. Å
230 pix
1.1 Å/pix.
= 253. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.1 Å
Contour Level:0.021 (by author), 0.021 (movie #1):
Minimum - Maximum-0.08127693 - 0.11371594
Average (Standard dev.)0.0023535916 (0.008607002)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 253 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z253.000253.000253.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0810.1140.002

Supplemental data

Sample components

Entire Watermelon mosaic virus

EntireName: Watermelon mosaic virus / Number of components: 3

Component #1: virus, Watermelon mosaic virus

VirusName: Watermelon mosaic virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Watermelon mosaic virus / virus

Component #2: protein, coat protein

ProteinName: coat protein
Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of being high flexible regions in the protein.
Recombinant expression: No
MassTheoretical: 31.463412 kDa
SourceSpecies: Watermelon mosaic virus / virus

Component #3: nucleic-acid, RNA (5'-R(P*UP*UP*UP*UP*U)-3')

Nucleic-acidName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / Class: RNA / Structure: OTHER / Synthetic: No
MassTheoretical: 1.485872 kDa
SourceSpecies: Watermelon mosaic virus / virus

Experimental details

Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 3.99 Å / Delta phi: -40.87 deg.
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

Atomic model buiding

Output model

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