[English] 日本語
Yorodumi
- PDB-3j0f: Sindbis virion -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3j0f
TitleSindbis virion
DescriptorCapsid protein
E1 envelope glycoprotein
E2 envelope glycoprotein
KeywordsVIRUS / alphavirus / virus assembly / glycoprotein
Specimen sourceSindbis virus / virus / SINV / シンドビスウイルス
MethodElectron microscopy (7 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsTang, J. / Jose, J. / Zhang, W. / Chipman, P. / Kuhn, R.J. / Baker, T.S.
CitationJ. Mol. Biol., 2011, 414, 442-459

J. Mol. Biol., 2011, 414, 442-459 StrPapers
Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.
Jinghua Tang / Joyce Jose / Paul Chipman / Wei Zhang / Richard J Kuhn / Timothy S Baker

DateDeposition: Jul 8, 2011 / Release: Oct 12, 2011 / Last modification: May 30, 2012

-
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-5251
  • 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
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)495,24212
Polyers495,24212
Non-polymers00
Water0
#1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein
x 60


Theoretical massNumber of molelcules
Total (without water)29,714,545720
Polyers29,714,545720
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
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein
x 5


  • icosahedral pentamer
  • 2.48 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,476,21260
Polyers2,476,21260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein
x 6


  • icosahedral 23 hexamer
  • 2.97 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,971,45472
Polyers2,971,45472
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 / Coat protein / C


Mass: 29410.232 Da / Num. of mol.: 4 / Fragment: UNP residues 1-264
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316, EC: 3.4.21.90

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
E1 envelope glycoprotein / Spike glycoprotein E1


Mass: 47417.285 Da / Num. of mol.: 4 / Fragment: UNP residues 807-1245
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)
E2 envelope glycoprotein / Spike glycoprotein E2


Mass: 46983.086 Da / Num. of mol.: 4 / Fragment: UNP residues 329-751
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

+
Experimental details

-
Experiment

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

-
Sample preparation

Assembly of specimenName: sindbis virion / Aggregation state: PARTICLE / Number of components: 60
ComponentName: alphavirus / Type: VIRUS
Details of the virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus host species: Homo sapiens / Virus isolate: STRAIN / Virus type: VIRION
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

EM imagingCamera length: 0 mm
MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Dec 12, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: eucentric / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: Kodak SO163 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 reconstructionResolution: 7 A
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 1KXF
Pdb chain id: A
Number of atoms included #LASTProtein: 4064 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4064

+
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