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- PDB-2xfc: CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST... -

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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 / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesCHIKUNGUNYA VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsVoss, J.E. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
Citation
Journal: Nature / Year: 2010
Title: Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
Authors: James E Voss / Marie-Christine Vaney / Stéphane Duquerroy / Clemens Vonrhein / Christine Girard-Blanc / Elodie Crublet / Andrew Thompson / Gérard Bricogne / Félix A Rey /
Abstract: Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is ...Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is mediated by two viral glycoproteins, E1 and E2, which carry the main antigenic determinants and form an icosahedral shell at the virion surface. Glycoprotein E2, derived from furin cleavage of the p62 precursor into E3 and E2, is responsible for receptor binding, and E1 for membrane fusion. In the context of a concerted multidisciplinary effort to understand the biology of CHIKV, here we report the crystal structures of the precursor p62-E1 heterodimer and of the mature E3-E2-E1 glycoprotein complexes. The resulting atomic models allow the synthesis of a wealth of genetic, biochemical, immunological and electron microscopy data accumulated over the years on alphaviruses in general. This combination yields a detailed picture of the functional architecture of the 25 MDa alphavirus surface glycoprotein shell. Together with the accompanying report on the structure of the Sindbis virus E2-E1 heterodimer at acidic pH (ref. 3), this work also provides new insight into the acid-triggered conformational change on the virus particle and its inbuilt inhibition mechanism in the immature complex.
#1: Journal: 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.
History
DepositionMay 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Derived calculations / Version format compliance
Revision 1.2Sep 25, 2013Group: Other
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / em_image_scans / Item: _cell.Z_PDB

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1015
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  • Superimposition on EM map
  • EMDB-1015
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polymers379,3408
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
Polymers22,760,405480
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
Polymers1,896,70040
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
Polymers2,276,04048
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
E1 ENVELOPE GLYCOPROTEIN


Mass: 47460.934 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 810-1248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Strain: 05-115 / Plasmid: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER (fruit fly) / Strain (production host): SCHNEIDER 2 / References: UniProt: Q1H8W5
#2: Protein
E2 ENVELOPE GLYCOPROTEIN


Mass: 47374.086 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 326-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Strain: 05-115 / Plasmid: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER (fruit fly) / Strain (production host): SCHNEIDER 2 / References: UniProt: Q1H8W5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

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

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Electron microscopy imaging

MicroscopyModel: 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 X / 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

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Processing

SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 9 Å / Num. 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
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22420 0 0 0 22420

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