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- EMDB-3693: Arabis Mosaic Virus capsid protein -

Open data

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Basic information

Database: EMDB / ID: 3693
TitleArabis Mosaic Virus capsid protein
Map data
SampleArabis mosaic virus (isolate Syrah):
virus / RNA2 polyprotein
SourceArabis mosaic virus (isolate Syrah)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsLecorre F
CitationJournal: To Be Published
Title: Arabis Mosaic Virus capsid protein
Authors: Lecorre F / Trapani S / Laikeehim J / Bron P
DateDeposition: Apr 26, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Oct 31, 2018 / Last update: Oct 31, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3693.map.gz (map file in CCP4 format, 322487 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
432 pix
1.08 Å/pix.
= 466.56 Å
432 pix
1.08 Å/pix.
= 466.56 Å
432 pix
1.08 Å/pix.
= 466.56 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Contour Level:0.5 (by author), 0.8 (movie #1):
Minimum - Maximum-4.8983555 - 7.3424706
Average (Standard dev.)0.0012315939 (0.34278435)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 466.56003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z466.560466.560466.560
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-215-216-216
D min/max/mean-4.8987.3420.001

Supplemental data

Sample components

Entire Arabis mosaic virus (isolate Syrah)

EntireName: Arabis mosaic virus (isolate Syrah) / Number of components: 2

Component #1: virus, Arabis mosaic virus (isolate Syrah)

VirusName: Arabis mosaic virus (isolate Syrah) / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Arabis mosaic virus (isolate Syrah)
Source (engineered)Expression System: Chenopodium quinoa
Source (natural)Host Species: Rubus odoratus

Component #2: protein, RNA2 polyprotein

ProteinName: RNA2 polyprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.765406 kDa
SourceSpecies: Arabis mosaic virus (isolate Syrah) / Strain: isolate Syrah
Source (engineered)Expression System: Chenopodium quinoa

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
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: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 16817
3D reconstructionSoftware: IMAGIC / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Cross-correlation coefficient / Refinement space: RECIPROCAL
Output model

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