[English] 日本語
Yorodumi
- PDB-3iym: Backbone Trace of the Capsid Protein Dimer of a Fungal Partitivir... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3iym
TitleBackbone Trace of the Capsid Protein Dimer of a Fungal Partitivirus from Electron Cryomicroscopy and Homology Modeling
DescriptorCapsid protein
KeywordsVIRUS / dsRNA virus / icosahedral virus / partitivirus / Penicillium stoloniferum virus S / PsV-S
Specimen sourcePenicillium stoloniferum virus S / virus
MethodElectron microscopy (4.7 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsTang, J. / Pan, J. / Havens, W.F. / Ochoa, W.F. / Li, H. / Sinkovits, R.S. / Guu, T.S.Y. / Ghabrial, S.A. / Nibert, M.L. / Tao, J.Y. / Baker, T.S.
CitationBiophys. J., 2010, 99, 685-694

Biophys. J., 2010, 99, 685-694 StrPapers
Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling.
Jinghua Tang / Junhua Pan / Wendy M Havens / Wendy F Ochoa / Tom S Y Guu / Said A Ghabrial / Max L Nibert / Yizhi Jane Tao / Timothy S Baker

DateDeposition: Feb 5, 2010 / Release: Jul 28, 2010 / Last modification: Nov 13, 2013

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5161
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5163
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)93,6622
Polyers93,6622
Non-polymers00
Water0
#1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,619,722120
Polyers5,619,722120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: Capsid protein
B: Capsid protein
x 5


  • icosahedral pentamer
  • 468 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)468,31010
Polyers468,31010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Capsid protein
B: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 562 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)561,97212
Polyers561,97212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

-
Components

#1: Polypeptide(L)Capsid protein


Mass: 46831.020 Da / Num. of mol.: 2 / Source: (natural) Penicillium stoloniferum virus S / virus / References: UniProt: Q6YDQ6

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenName: PsV-S / Aggregation state: PARTICLE / Number of components: 1
ComponentName: PsV-S / Details: authentic virus particles / Type: VIRUS
Details of the virusEmpty: NO / Enveloped: NO / Virus host category: FUNGI / Virus host growth cell: Penicillium stoloniferum / Virus host species: Fungi / Virus isolate: SPECIES / Virus type: VIRION
Buffer solutionName: 50mM Tris pH7.6, 150mM NaCl, 5mM EDTA, 1mM DTT
Sample preparationpH: 7.6 / Sample conc.: 5 mg/ml
VitrificationCryogen name: ETHANE / Temp: 89 K / Humidity: 80 / Method: blot for 7.5 seconds before plunging

-
Electron microscopy imaging

EM imagingCamera length: 0 mm
MicroscopyMicroscope model: TECNAI G2
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2.2 nm / Nominal defocus min: 1.4 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Temperature: 77 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO-163 electron-image FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionSoftware: AUTO3DEM / Resolution: 4.7 A / Number of particles: 14252 / Nominal pixel size: 1.27 A/pix / Actual pixel size: 1.27 A/pix
Number of atoms included #LASTProtein: 3168 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3168

+
About Yorodumi

-
News

-
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

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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 / Changes in new EM Navigator and Yorodumi

Read more