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- EMDB-10001: CryoEM structure of modified Turnip Yellows Virus devoid of minor... -

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Basic information

Entry
Database: EMDB / ID: EMD-10001
TitleCryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain
Map dataSharpened map
Sample
  • Virus: Beet western yellows virus-FL1
    • Protein or peptide: Major capsid protein
Keywordsvirus
Function / homologyLuteovirus group 1 coat protein / Luteovirus coat protein / T=3 icosahedral viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesTurnip yellows virus (isolate FL-1) / Beet western yellows virus-FL1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsTrapani S / Lai Kee Him J
Funding support France, 1 items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05 France
CitationJournal: To Be Published
Title: CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain
Authors: Trapani S / Lai Kee Him J / Boissinot S / Reinbold C / Fallet C / Ancelin A / Lecorre F / Hoh F / Ziegler-Graff V / Brault V / Bron P
History
DepositionMay 24, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseJul 8, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rtk
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rtk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10001.png

Downloads & links

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Map

FileDownload / File: emd_10001.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 380 pix.
= 465.5 Å		1.23 Å/pix.
x 380 pix.
= 465.5 Å		1.23 Å/pix.
x 380 pix.
= 465.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.225 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.011
Minimum - Maximum-0.029754454 - 0.05907673
Average (Standard dev.)0.00001867729 (±0.0036415805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 465.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2251.2251.225
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z465.500465.500465.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0300.0590.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_10001_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1 map

Fileemd_10001_half_map_1.map
Annotationhalf_1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_10001_half_map_2.map
Annotationhalf_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 : Beet western yellows virus-FL1

EntireName: Beet western yellows virus-FL1
Components
  • Virus: Beet western yellows virus-FL1
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Beet western yellows virus-FL1

SupramoleculeName: Beet western yellows virus-FL1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12043 / Sci species name: Beet western yellows virus-FL1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: capsid / T number (triangulation number): 3

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Turnip yellows virus (isolate FL-1) / Strain: isolate FL-1
Molecular weightTheoretical: 22.52252 KDa
SequenceString: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVFS KDNLAGSSSG AITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS SQNSGSIAYE LDPHCKLNSL SSTINKFGIT KPGKRAFTAS Y INGTEWHD ...String:
MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVFS KDNLAGSSSG AITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS SQNSGSIAYE LDPHCKLNSL SSTINKFGIT KPGKRAFTAS Y INGTEWHD VAEDQFRILY KGNGSSSIAG SFRITIKCQF HNPK

UniProtKB: Major capsid protein

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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

Concentration3.5 mg/mL
BufferpH: 6 / Component - Concentration: 0.1 mol / L / Component - Name: citrate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 3003
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6rtk:
CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain

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