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- EMDB-3693: Arabis Mosaic Virus capsid protein -

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Basic information

Entry
Database: EMDB / ID: EMD-3693
TitleArabis Mosaic Virus capsid protein
Map data
Sample
  • Virus: Arabis mosaic virus (isolate Syrah)
    • Protein or peptide: RNA2 polyprotein
Biological speciesArabis mosaic virus (isolate Syrah)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLecorre F
CitationJournal: To Be Published
Title: Arabis Mosaic Virus capsid protein
Authors: Lecorre F / Trapani S / Laikeehim J / Bron P
History
DepositionApr 26, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseOct 31, 2018-
UpdateFeb 27, 2019-
Current statusFeb 27, 2019Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3693.png

Downloads & links

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Map

FileDownload / File: emd_3693.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.8
Minimum - Maximum-4.8983555 - 7.3424706
Average (Standard dev.)0.0012315939 (±0.34278435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-215-216
Dimensions432432432
Spacing432432432
CellA=B=C: 466.56003 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS-215-216-216
NC/NR/NS432432432
D min/max/mean-4.8987.3420.001

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Supplemental data

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Half map: #2

Fileemd_3693_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_3693_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabis mosaic virus (isolate Syrah)

EntireName: Arabis mosaic virus (isolate Syrah)
Components
  • Virus: Arabis mosaic virus (isolate Syrah)
    • Protein or peptide: RNA2 polyprotein

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Supramolecule #1: Arabis mosaic virus (isolate Syrah)

SupramoleculeName: Arabis mosaic virus (isolate Syrah) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 283676 / Sci species name: Arabis mosaic virus (isolate Syrah) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Rubus odoratus (flowering raspberry)
Host (natural)Organism: Rheum rhabarbarum (garden rhubarb)
Host systemOrganism: Chenopodium quinoa (quinoa)

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Macromolecule #1: RNA2 polyprotein

MacromoleculeName: RNA2 polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabis mosaic virus (isolate Syrah) / Strain: isolate Syrah
Molecular weightTheoretical: 55.765406 KDa
Recombinant expressionOrganism: Chenopodium quinoa (quinoa)
SequenceString: GLAGRGTVPV PKDCQAGKYL KTLDLRDMVS GFSGIQYEKW ITAGLVMPDF KVVIRYPANA FTGITWVMSF DAYNRITSSI STTASPAYT LSVPHWLLHH KNGTTSCDID YGELCGHAMW FSATTFESPK LHFTCLTGNN KELAADWEFV VELYAEFEAA K SFLGKPNF ...String:
GLAGRGTVPV PKDCQAGKYL KTLDLRDMVS GFSGIQYEKW ITAGLVMPDF KVVIRYPANA FTGITWVMSF DAYNRITSSI STTASPAYT LSVPHWLLHH KNGTTSCDID YGELCGHAMW FSATTFESPK LHFTCLTGNN KELAADWEFV VELYAEFEAA K SFLGKPNF IYSADAFNGS LKFLTIPPLE YDLSATSAYK SVSLLLGQTL VDGTHKVYNF NNTLLSYYLG IGGIVKGKVH VC SPCTYGI VLRVVSEWNG VTNNWNQLFK YPGCYIEEDG SFAIEIRSPY HRTPLRLIDA QSASSFTSTL NFYAISGPIA PSG ETAKMP VVVQIEEIAL PDLSVPSFPN DYFLWVDFSS FTVDVEEYVI GSRFFDISST TSTVALGDNP FSHMIACHGL HHGI LDLKL MWDLEGEFGK SSGGVTITKL CGDKATGMDG ASRVCALQNM GCETELYIGN YAGANPNTAL SLYSRWLAIK LDKAK SMKM LRILCKPRGN FEFYGRTCFK V

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
15.0 mMNa2HPO4Sodium phosphate
5.0 mMK2HPO4Potassium phosphate
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: IMAGIC (ver. 4-D)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMAGIC (ver. 4-D) / Number images used: 16817
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 4-D)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 4-D)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model


PDB Unreleased entry

PDB-5nsi:
Arabis Mosaic Virus capsid protein

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