[English] 日本語
Yorodumi
- EMDB-8609: Cleaved Cowpea Mosaic Virus (CPMV) eVLP structure refined from a ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8609
TitleCleaved Cowpea Mosaic Virus (CPMV) eVLP structure refined from a small subset of data from the cryo-EM reconstruction of uncleaved eVLP reported previously
Map dataCowpea mosaic virus (CPMV) cleaved eVLP structure
SampleCowpea mosaic virus
  • virus
Function/homologyRNA2 polyprotein / Large coat protein / Large coat protein / transport of virus in host, cell to cell / host cell plasmodesma / Small coat protein / viral capsid / GTP binding / structural molecule activity / RNA binding ...RNA2 polyprotein / Large coat protein / Large coat protein / transport of virus in host, cell to cell / host cell plasmodesma / Small coat protein / viral capsid / GTP binding / structural molecule activity / RNA binding / DNA binding / | / RNA2 polyprotein
Function and homology information
SourceCowpea mosaic virus / / virus
MethodCryo EM / single particle (icosahedral) reconstruction / 4.4 Å resolution
AuthorsHesketh EL / Thompson RF / Ranson NA
CitationJournal: Sci Rep / Year: 2017
Title: The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy.
Authors: Emma L Hesketh / Yulia Meshcheriakova / Rebecca F Thompson / George P Lomonossoff / Neil A Ranson
Abstract: Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. ...Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation. This work has furthered our knowledge of Picornavirales genome encapsidation and will assist further work in the development of CPMV as a biotechnological tool.
DateDeposition: Feb 20, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 12, 2017 / Last update: Jan 31, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

-
Map

Fileemd_8609.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.04 Å/pix.
= 499.2 Å
480 pix
1.04 Å/pix.
= 499.2 Å
480 pix
1.04 Å/pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.0803581 - 0.20112681
Average (Standard dev.)0.0021032945 (0.012859347)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0800.2010.002

-
Supplemental data

-
Sample components

-
Entire Cowpea mosaic virus

EntireName: Cowpea mosaic virus
Details: Empty virus like particles (eVLPs) produced by expressing a coat precursor protein VP60 which expressed both large and small proteins and the 24K protease in N. benthamiana
Number of components: 1
MassTheoretical: 3.87 MDa

-
Component #1: virus, Cowpea mosaic virus

VirusName: Cowpea mosaic virus / Class: VIRUS-LIKE PARTICLE
Details: Empty virus like particles (eVLPs) produced by expressing a coat precursor protein VP60 which expressed both large and small proteins and the 24K protease in N. benthamiana
Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 3.87 MDa
SpeciesSpecies: Cowpea mosaic virus / / virus
Source (engineered)Expression System: Nicotiana benthamiana / / plant / image: Nicotiana tabacum
Source (natural)Host Species: Vigna unguiculata / Cowpea / plant

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionSpecimen conc.: 4.2 mg/ml / Buffer solution: Phosphate buffer pH 7.0 / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 94 K / Humidity: 100 %

-
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: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 134615 X (nominal), 134615 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90 - 90 K)
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1135

-
Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1537
3D reconstructionSoftware: RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more