[English] 日本語
Yorodumi
- PDB-2xfc: CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2xfc
TitleCHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST VIRUS cryo-EM MAP
Components
  • E1 ENVELOPE GLYCOPROTEIN
  • E2 ENVELOPE GLYCOPROTEIN
KeywordsVIRUS / RECEPTOR BINDING / MEMBRANE FUSION / ICOSAHEDRAL ENVELOPED VIRUS
Function/homologyAlphavirus E2 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Peptidase S3, togavirin / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E3 glycoprotein / Flavivirus glycoprotein, central and dimerisation domain superfamily ...Alphavirus E2 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Peptidase S3, togavirin / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E3 glycoprotein / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / host cell membrane / viral capsid / Immunoglobulin E-set / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / virion membrane / Peptidase S1, PA clan / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / identical protein binding / Structural polyprotein
Function and homology information
Specimen sourceCHIKUNGUNYA VIRUS / virus / Chikungunya
MethodElectron microscopy (9 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsVoss, J.E. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
CitationJournal: Mol. Cell / Year: 2000
Title: Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus.
Authors: E J Mancini / M Clarke / B E Gowen / T Rutten / S D Fuller
Abstract: Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion ...Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion structure to 9 A resolution. The improved resolution of this map reveals an N-terminal arm linking capsid subunits and defines the spike-capsid interaction sites. It illustrates the paired helical nature of the transmembrane segments and the elongated structures connecting them to the spike projecting domains. A 10 A diameter density in the fusion protein lines the cavity at the center of the spike. These clearly visible features combine with the variation in order between the layers to provide a framework for understanding the structural changes during the life cycle of an enveloped virus.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 21, 2010 / Release: Nov 24, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 24, 2010Structure modelrepositoryInitial release
1.1Apr 3, 2013Structure modelDerived calculations / Version format compliance
1.2Sep 25, 2013Structure modelOther

-
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-1015
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links

-
Assembly

Deposited unit
A: E1 ENVELOPE GLYCOPROTEIN
B: E2 ENVELOPE GLYCOPROTEIN
D: E1 ENVELOPE GLYCOPROTEIN
E: E2 ENVELOPE GLYCOPROTEIN
F: E1 ENVELOPE GLYCOPROTEIN
G: E2 ENVELOPE GLYCOPROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)379,3408
Polyers379,3408
Non-polymers00
Water0
1
A: E1 ENVELOPE GLYCOPROTEIN
B: E2 ENVELOPE GLYCOPROTEIN
D: E1 ENVELOPE GLYCOPROTEIN
E: E2 ENVELOPE GLYCOPROTEIN
F: E1 ENVELOPE GLYCOPROTEIN
G: E2 ENVELOPE GLYCOPROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)22,760,405480
Polyers22,760,405480
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: E1 ENVELOPE GLYCOPROTEIN
B: E2 ENVELOPE GLYCOPROTEIN
D: E1 ENVELOPE GLYCOPROTEIN
E: E2 ENVELOPE GLYCOPROTEIN
F: E1 ENVELOPE GLYCOPROTEIN
G: E2 ENVELOPE GLYCOPROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
x 5


  • icosahedral pentamer
  • 1.9 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,896,70040
Polyers1,896,70040
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E1 ENVELOPE GLYCOPROTEIN
B: E2 ENVELOPE GLYCOPROTEIN
D: E1 ENVELOPE GLYCOPROTEIN
E: E2 ENVELOPE GLYCOPROTEIN
F: E1 ENVELOPE GLYCOPROTEIN
G: E2 ENVELOPE GLYCOPROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
x 6


  • icosahedral 23 hexamer
  • 2.28 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)2,276,04048
Polyers2,276,04048
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


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

-
Components

#1: Protein/peptide
E1 ENVELOPE GLYCOPROTEIN


Mass: 47460.934 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 810-1248
Source: (gene. exp.) CHIKUNGUNYA VIRUS / virus / Chikungunya
Strain: 05-115 / Plasmid name: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER / Strain (production host): SCHNEIDER 2 / References: UniProt:Q1H8W5
#2: Protein/peptide
E2 ENVELOPE GLYCOPROTEIN


Mass: 47374.086 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 326-748
Source: (gene. exp.) CHIKUNGUNYA VIRUS / virus / Chikungunya
Strain: 05-115 / Plasmid name: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER / Strain (production host): SCHNEIDER 2 / References: UniProt:Q1H8W5

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: semliki forest virus / Type: VIRUS
Buffer solutionDetails: Tris (10mM) NaCl (100 mM) ph 7.4 / pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG/ST / Date: Jan 1, 1995
Electron gunElectron source: OTHER / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 50000 / Nominal defocus max: 7628 nm / Nominal defocus min: 975 nm
Image recordingElectron dose: 8 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

-
Processing

SymmetryPoint symmetry: I
3D reconstructionResolution: 9 Å / Number of particles: 6000
Details: THE COMPLETE PARTICLE IS GENERATED BY BIOMT MATRICES. THE FIT WAS GENERATED WITH URO IN SINDBIS CRYO-EM MAP EMDB-1015 THAT WAS CORRECTED IN MAGNITUDE BY MULTIPLYING A FACTOR OF 1.038 AND USING PDB ENTRY 3N40
Symmetry type: POINT
Least-squares processHighest resolution: 9 Å
Refine hist #LASTHighest resolution: 9 Å
Number of atoms included #LASTProtein: 22420 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 22420

+
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 / 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

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 / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more