[English] 日本語
Yorodumi
- EMDB-3562: Cowpea mosaic virus top component (CPMV-T) - naturally occurring ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3562
TitleCowpea mosaic virus top component (CPMV-T) - naturally occurring empty particles
Map dataThe naturally occurring empty cowpea mosaic virus capsid (CPMV-T)
Sample
  • Virus: Cowpea mosaic virus
    • Protein or peptide: Small subunit of cowpea mosaic virus
    • Protein or peptide: Large subunit of Cowpea music virus
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesCowpea mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsHesketh EL / Meshcheriakova Y / Thompson RF / Lomonossoff GP / Ranson NA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L020955/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 United Kingdom
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.
History
DepositionDec 29, 2016-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5ms1
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ms1
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3562.png

Downloads & links

-
Map

FileDownload / File: emd_3562.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe naturally occurring empty cowpea mosaic virus capsid (CPMV-T)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.36318156 - 0.5396457
Average (Standard dev.)0.0005197688 (±0.027992168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 1.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z492.800492.800492.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.3630.5400.001

-
Supplemental data

-
Sample components

-
Entire : Cowpea mosaic virus

EntireName: Cowpea mosaic virus
Components
  • Virus: Cowpea mosaic virus
    • Protein or peptide: Small subunit of cowpea mosaic virus
    • Protein or peptide: Large subunit of Cowpea music virus

-
Supramolecule #1: Cowpea mosaic virus

SupramoleculeName: Cowpea mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12264 / Sci species name: Cowpea mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Vigna unguiculata (cowpea)

-
Macromolecule #1: Small subunit of cowpea mosaic virus

MacromoleculeName: Small subunit of cowpea mosaic virus / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cowpea mosaic virus
Molecular weightTheoretical: 23.798902 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: GPVCAEASDV YSPCMIASTP PAPFSDVTAV TFDLINGKIT PVGDDNWNTH IYNPPIMNVL RTAAWKSGTI HVQLNVRGAG VKRADWDGQ VFVYLRQSMN PESYDARTFV ISQPGSAMLN FSFDIIGPNS GFEFAESPWA NQTTWYLECV ATNPRQIQQF E VNMRFDPN ...String:
GPVCAEASDV YSPCMIASTP PAPFSDVTAV TFDLINGKIT PVGDDNWNTH IYNPPIMNVL RTAAWKSGTI HVQLNVRGAG VKRADWDGQ VFVYLRQSMN PESYDARTFV ISQPGSAMLN FSFDIIGPNS GFEFAESPWA NQTTWYLECV ATNPRQIQQF E VNMRFDPN FRVAGNILMP PFPLSTETPP LLKFRFRDIE RSKRSVMVQH TATAA

-
Macromolecule #2: Large subunit of Cowpea music virus

MacromoleculeName: Large subunit of Cowpea music virus / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cowpea mosaic virus
Molecular weightTheoretical: 40.858434 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MEQNLFALSL DDTSSVRGSL LDTKFAQTRV LLSKAMAGGD VLLDEYLYDV VNGQDFRATV AFLRTHVITG KIKVTATTNI SDNSGCCLM LAINSGVRGK YSTDVYTICS QDSMTWNPGC KKNFSFTFNP NPCGDSWSAE MISRSRVRMT VICVSGWTLS P TTDVIAKL ...String:
MEQNLFALSL DDTSSVRGSL LDTKFAQTRV LLSKAMAGGD VLLDEYLYDV VNGQDFRATV AFLRTHVITG KIKVTATTNI SDNSGCCLM LAINSGVRGK YSTDVYTICS QDSMTWNPGC KKNFSFTFNP NPCGDSWSAE MISRSRVRMT VICVSGWTLS P TTDVIAKL DWSIVNEKCE PTIYHLADCQ NWLPLNRWMG KLTFPQGVTS EVRRMPLSIG GGAGATQAFL ANMPNSWISM WR YFRGELH FEVTKMSSPY IKATVTFLIA FGNLSDAFGF YESFPHRIVQ FAEVEEKCTL VFSQQEFVTA WSTQVNPRTT LEA DGCPYL YAIIHDSTTG TISGDFNLGV KLVGIKDFCG IGSNPGIDGS RLL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.92 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 10.0 µm / Nominal defocus min: 0.35 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1323 / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 5594
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

3014

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 4696
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-5ms1:
Cowpea mosaic virus top component (CPMV-T) - naturally occurring empty particles

+
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