[English] 日本語
Yorodumi
- EMDB-3785: Structure of Watermelon mosaic virus potyvirus. -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3785
TitleStructure of Watermelon mosaic virus potyvirus.
Map dataCryoelectron microscopy map of Watermelon mosaic virus filament. Resulting map from Relion postprocessing.
SampleWatermelon mosaic virus:
virus / coat protein / nucleic-acidNucleic acid
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Polyprotein
Function and homology information
SourceWatermelon mosaic virus
Methodhelical reconstruction / cryo EM / 4 Å resolution
AuthorsZamora M / Mendez-Lopez E
CitationJournal: Sci Adv / Year: 2017
Title: Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses.
Authors: Miguel Zamora / Eduardo Méndez-López / Xabier Agirrezabala / Rebeca Cuesta / José L Lavín / M Amelia Sánchez-Pina / Miguel A Aranda / Mikel Valle
Validation ReportPDB-ID: 5odv

SummaryFull reportAbout validation report
DateDeposition: Jul 6, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Sep 27, 2017 / Last update: Oct 11, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5odv
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5odv
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3785.map.gz (map file in CCP4 format, 48669 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
230 pix
1.1 Å/pix.
= 253. Å
230 pix
1.1 Å/pix.
= 253. Å
230 pix
1.1 Å/pix.
= 253. 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 Level:0.021 (by author), 0.021 (movie #1):
Minimum - Maximum-0.08127693 - 0.11371594
Average (Standard dev.)0.0023535916 (0.008607002)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions230230230
Origin000
Limit229229229
Spacing230230230
CellA=B=C: 253 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z253.000253.000253.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0810.1140.002

-
Supplemental data

-
Sample components

-
Entire Watermelon mosaic virus

EntireName: Watermelon mosaic virus / Number of components: 3

-
Component #1: virus, Watermelon mosaic virus

VirusName: Watermelon mosaic virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Watermelon mosaic virus

-
Component #2: protein, coat protein

ProteinName: coat protein
Details: 57 residues from N-terminus and 17 residues from C-terminus are not present in our pdb model due to the absence of densities for them in the cryo-electron microscopy map as a consequence of being high flexible regions in the protein.
Recombinant expression: No
MassTheoretical: 31.463412 kDa
SourceSpecies: Watermelon mosaic virus

-
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 / Structure: OTHER / Synthetic: No
Sequence:
UUUUU
MassTheoretical: 1.485872 kDa
SourceSpecies: Watermelon mosaic virus

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 3.99 Å / Delta phi: -40.87 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: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
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

+
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

+
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.
  • 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