[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 dataCryoEM map for Turnip mosaic virus (TuMV)
Sample
  • Virus: Turnip mosaic virus
    • Protein or peptide: Coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Keywordspotyvirus / virion / helical virus / VIRUS
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein / Genome polyprotein
Function and homology information
Biological speciesTurnip mosaic virus (strain Japanese) / Turnip mosaic 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.
History
DepositionOct 10, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing 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

emd_10373.png

Downloads & links

-
Map

FileDownload / File: emd_10373.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map for Turnip mosaic virus (TuMV)
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

Histogram

Histogram (log scale)
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
Components
  • Virus: Turnip mosaic virus
    • Protein or peptide: Coat protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

-
Supramolecule #1: Turnip mosaic virus

SupramoleculeName: Turnip mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12230 / Sci species name: Turnip mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Brassica rapa subsp. rapa (turnip)

-
Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Turnip mosaic virus (strain Japanese) / Strain: Japanese
Molecular weightTheoretical: 24.073395 KDa
SequenceString: PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT EDKMQIILNG LMVWCIENGT SPNINGMWV MMDGDDQVEF PIKPLIDHAK PTFRQIMAHF SDVAEAYIEK RNQDRPYMPR YGLQRNLTDM SLARYAFDFY E MTSRTPIR ...String:
PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT EDKMQIILNG LMVWCIENGT SPNINGMWV MMDGDDQVEF PIKPLIDHAK PTFRQIMAHF SDVAEAYIEK RNQDRPYMPR YGLQRNLTDM SLARYAFDFY E MTSRTPIR AREAHIQMKA AALRGANNNL FGLDGNVGTT VENTERHTT

UniProtKB: Genome polyprotein

-
Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Details: Model of ssRNA as polyU / Number of copies: 19
Source (natural)Organism: Turnip mosaic virus
Molecular weightTheoretical: 1.485872 KDa
SequenceString:
UUUUU

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-31 / Number grids imaged: 1 / Average exposure time: 9.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 194432
Segment selectionNumber selected: 444678 / Software - Name: RELION (ver. 2)
Startup modelType of model: INSILICO MODEL
In silico model: Cylinder with the diameter of the filament.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)

-
Atomic model buiding 1

Initial modelPDB ID:

5odv


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 270
Output model

PDB-6t34:
Atomic model for Turnip mosaic virus (TuMV)

+
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