[English] 日本語
Yorodumi
- EMDB-4504: Cryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4504
TitleCryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV)
Map datasharpened map
Sample
  • Virus: Broad bean stain virus
    • Protein or peptide: Large coat-protein subunit
    • Protein or peptide: Small coat-protein subunit
Keywordscomovirus capsid plant virus BBSV / virus
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / GTP binding / structural molecule activity / DNA binding / RNA binding / membrane
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesBroad bean stain virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsLecorre F / Lai Jee Him J / Blanc S
Funding supportNew Caledonia, France, 3 items
OrganizationGrant numberCountry
Government of New CaledoniaNew Caledonia
French Infrastructure for Integrated Structural BiologyANR-10-INBS-05 France
France BioImaging (FBI)ANR-10-INBS-04-01 France
CitationJournal: Virology / Year: 2019
Title: The cryo-electron microscopy structure of Broad Bean Stain Virus suggests a common capsid assembly mechanism among comoviruses.
Authors: François Lecorre / Joséphine Lai-Kee-Him / Stéphane Blanc / Jean-Louis Zeddam / Stefano Trapani / Patrick Bron /
Abstract: The Broad bean stain virus (BBSV) is a member of the genus Comovirus infecting Fabaceae. The virus is transmitted through seed and by plant weevils causing severe and widespread disease worldwide. ...The Broad bean stain virus (BBSV) is a member of the genus Comovirus infecting Fabaceae. The virus is transmitted through seed and by plant weevils causing severe and widespread disease worldwide. BBSV has a bipartite, positive-sense, single-stranded RNA genome encapsidated in icosahedral particles. We present here the cryo-electron microscopy reconstruction of the BBSV and an atomic model of the capsid proteins refined at 3.22 Å resolution. We identified residues involved in RNA/capsid interactions revealing a unique RNA genome organization. Inspection of the small coat protein C-terminal domain highlights a maturation cleavage between Leu567 and Leu568 and interactions of the C-terminal stretch with neighbouring small coat proteins within the capsid pentameric turrets. These interactions previously proposed to play a key role in the assembly of the Cowpea mosaic virus suggest a common capsid assembly mechanism throughout all comovirus species.
History
DepositionDec 27, 2018-
Header (metadata) releaseJan 9, 2019-
Map releaseMay 1, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qcc
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qcc
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4504.png

Downloads & links

-
Map

FileDownload / File: emd_4504.map.gz / Format: CCP4 / Size: 476.8 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.)
1.11 Å/pix.
x 500 pix.
= 555. Å		1.11 Å/pix.
x 500 pix.
= 555. Å		1.11 Å/pix.
x 500 pix.
= 555. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.202414 - 0.29871136
Average (Standard dev.)0.00017448509 (±0.013553439)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 555.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z555.000555.000555.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.2020.2990.000

-
Supplemental data

-
Additional map: unsharpened map

Fileemd_4504_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_4504_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_4504_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Broad bean stain virus

EntireName: Broad bean stain virus
Components
  • Virus: Broad bean stain virus
    • Protein or peptide: Large coat-protein subunit
    • Protein or peptide: Small coat-protein subunit

-
Supramolecule #1: Broad bean stain virus

SupramoleculeName: Broad bean stain virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 593572 / Sci species name: Broad bean stain virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vicia faba (fava bean)
Virus shellShell ID: 1 / Name: capsid / Diameter: 300.0 Å / T number (triangulation number): 1

-
Macromolecule #1: Large coat-protein subunit

MacromoleculeName: Large coat-protein subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Broad bean stain virus
Molecular weightTheoretical: 41.247977 KDa
SequenceString: MDVDLFKLSL DDTSSVKGSL LDTRFAQVRV VIPKAMAGGN ELLNSNLYDI LVVDNNFRAA AALAHTHIIE GQIKCVCTIN LPENTGCCL ALCVNSSNRG QFSTDIYTIG SQDRMLWNPA CSKNSTFTFN PNPCGTGWSL EFLRRTKFHI SVVCVSGWSA Q PQTDLVMT ...String:
MDVDLFKLSL DDTSSVKGSL LDTRFAQVRV VIPKAMAGGN ELLNSNLYDI LVVDNNFRAA AALAHTHIIE GQIKCVCTIN LPENTGCCL ALCVNSSNRG QFSTDIYTIG SQDRMLWNPA CSKNSTFTFN PNPCGTGWSL EFLRRTKFHI SVVCVSGWSA Q PQTDLVMT MDFFVANVPC VPRIYNLGSP GQTLWLNRWM GKLSFGQGVS NDIKSMPLAI GGGAGAKDSI LMNMTNAYLS LW RYFHGDL VFEVNKMSSP YIKSTVTFFI GFGGVSFQPE LEDFPNKLVQ FSEVQEKIEL KFTRAEFLTA WSTQVDPAAQ LAN DGCPYL YAMVHDSTAS TIVGDFNLGV TLTRIENFAG IGCNPGIQGA RLLGSAIATP Q

UniProtKB: RNA2 polyprotein

-
Macromolecule #2: Small coat-protein subunit

MacromoleculeName: Small coat-protein subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Broad bean stain virus
Molecular weightTheoretical: 23.589662 KDa
SequenceString: NAVVRSSPGI YSNCFSLRAP LKPDGPKSFT CDLMGGGVVT DGDTGWQVTV RNTPVSNLLR TAAWKRGTVH VQVVLAGASV KRSDWDSTV QIFLRQSMAT SSYDAKIWDI CQPGAAMLEF SFDVVGPNSG FEMWDSNWAS QTSWFLEFLI SNPAQNTLFE V NLRLDENF ...String:
NAVVRSSPGI YSNCFSLRAP LKPDGPKSFT CDLMGGGVVT DGDTGWQVTV RNTPVSNLLR TAAWKRGTVH VQVVLAGASV KRSDWDSTV QIFLRQSMAT SSYDAKIWDI CQPGAAMLEF SFDVVGPNSG FEMWDSNWAS QTSWFLEFLI SNPAQNTLFE V NLRLDENF SVAGTTLMPP FVLDRVSVAR PLLGKQTKTV ARSARVVRET KEASESP

UniProtKB: RNA2 polyprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.4 / Component - Concentration: 20.0 mM / Component - Formula: K2HPO4/KH2PO4 / Component - Name: Phosphate
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 298.15 K / Instrument: GATAN CRYOPLUNGE 3 / Details: blot for 1 second before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Digitization - Frames/image: 3-9 / Number grids imaged: 1 / Number real images: 2899 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2 / Details: 1494 images were retained for 3D reconstruction
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 35663
Startup modelType of model: INSILICO MODEL / In silico model: Generated by RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 17233
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0-beta-2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta-2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0-beta-2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1ny7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6qcc:
Cryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more