[English] 日本語
Yorodumi
- EMDB-10373: CryoEM structure for Turnip mosaic virus (TuMV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10373
TitleCryoEM structure for Turnip mosaic virus (TuMV)
Map data
SampleTurnip mosaic virus:
virus / Coat protein / nucleic-acidNucleic acid
Function / homologyPotyvirus coat protein / viral capsid / Coat protein / Coat protein
Function and homology information
Biological speciesTurnip mosaic virus / TuMV (virus)
Methodhelical reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsValle MV / Cuesta R
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098996-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2015-66326-P Spain
CitationJournal: Sci Rep / Year: 2019
Title: Structure of Turnip mosaic virus and its viral-like particles.
Authors: Rebeca Cuesta / Carmen Yuste-Calvo / David Gil-Cartón / Flora Sánchez / Fernando Ponz / Mikel Valle /
Abstract: Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide ...Turnip mosaic virus (TuMV), a potyvirus, is a flexible filamentous plant virus that displays a helical arrangement of coat protein copies (CPs) bound to the ssRNA genome. TuMV is a bona fide representative of the Potyvirus genus, one of most abundant groups of plant viruses, which displays a very wide host range. We have studied by cryoEM the structure of TuMV virions and its viral-like particles (VLPs) to explore the role of the interactions between proteins and RNA in the assembly of the virions. The results show that the CP-RNA interaction is needed for the correct orientation of the CP N-terminal arm, a region that plays as a molecular staple between CP subunits in the fully assembled virion.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionOct 10, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6t34
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6t34
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_10373.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 250 pix.
= 275. Å
1.1 Å/pix.
x 250 pix.
= 275. Å
1.1 Å/pix.
x 250 pix.
= 275. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0832917 - 0.14232388
Average (Standard dev.)0.003384128 (±0.013149834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 275.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z275.000275.000275.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0830.1420.003

-
Supplemental data

-
Sample components

-
Entire Turnip mosaic virus

EntireName: Turnip mosaic virus / Number of components: 3

-
Component #1: virus, Turnip mosaic virus

VirusName: Turnip mosaic virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Turnip mosaic virus
Source (natural)Host Species: Brassica rapa subsp. rapa (turnip)

-
Component #2: protein, Coat protein

ProteinName: Coat protein / Number of Copies: 19 / Recombinant expression: No
MassTheoretical: 24.073395 kDa
SourceSpecies: TuMV (virus) / Strain: Japanese

-
Component #3: nucleic-acid, RNA (5'-R(P*UP*UP*UP*UP*U)-3')

nucleic acidName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / Class: RNA / Details: Model of ssRNA as polyU / Structure: OTHER / Synthetic: No
Sequence:
UUUUU
MassTheoretical: 1.485872 kDa
SourceSpecies: Turnip mosaic virus

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4 Å / Delta phi: -40.8 %deg;
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 5ODV
Chain ID: A

Overall bvalue: 270
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. 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

Read more

-
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.

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