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- PDB-2xfb: CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SINDBIS VIRUS ... -

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Basic information

Entry
Database: PDB / ID: 2xfb
TitleCHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SINDBIS VIRUS cryo- EM MAP
Components
  • E1 ENVELOPE GLYCOPROTEIN
  • E2 ENVELOPE GLYCOPROTEIN
KeywordsVIRUS / ALPHAVIRUS / 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: Structure / Year: 2006
Title: Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
Authors: Suchetana Mukhopadhyay / Wei Zhang / Stefan Gabler / Paul R Chipman / Ellen G Strauss / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann /
Abstract: The 9 A resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and ...The 9 A resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and E2 glycoproteins in the formation of a heterodimer, on the difference in conformation of the two types of trimeric spikes, on the interaction between the transmembrane helices of the E1 and E2 proteins, and on the conformational changes that occur when fusing with a host cell. The positions of various markers on the E2 protein established the approximate topology of the E2 structure. The largest conformational differences between the icosahedral surface spikes at icosahedral 3-fold and quasi-3-fold positions are associated with the monomers closest to the 5-fold axes. The long E2 monomers, containing the cell receptor recognition motif at their extremities, are shown to rotate by about 180 degrees and to move away from the center of the spikes during fusion.
History
DepositionMay 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Oct 23, 2019Group: Data collection / Other / Category: cell / em_image_scans / Item: _cell.Z_PDB

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Structure visualization

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  • 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-1121
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  • Superimposition on EM map
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Structure viewerMolecule:
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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)320,7038
Polymers320,7038
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)19,242,178480
Polymers19,242,178480
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
  • 1.6 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,603,51540
Polymers1,603,51540
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
  • 1.92 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,924,21848
Polymers1,924,21848
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: 42554.148 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: 37621.594 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: Sindbis virus / Type: VIRUS
Buffer solutionpH: 7.4 / Details: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
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 CM200T / Date: Jun 21, 2000
Electron gunElectron source: OTHER / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 38000 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 18 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: 7085
Details: THE COMPLETE PARTICLE IS GENERATED BY BIOMT MATRICES. THE FIT WAS GENERATED WITH URO IN SINDBIS CRYO-EM MAP EMDB-1121 USING PDB ENTRY 3N40.
Symmetry type: POINT
Atomic model buildingPDB-ID: 3N40
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22460 0 0 0 22460

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