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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 / homologyAlphavirus E2 glycoprotein / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily ...Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus core protein / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / identical protein binding / Structural polyprotein
Function and homology information
Specimen sourceCHIKUNGUNYA VIRUS / Chikungunya / virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9 Å resolution
AuthorsVoss, J.E. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 21, 2010 / Release: Nov 24, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 24, 2010Structure modelrepositoryInitial release
1.1Mar 20, 2013Structure modelDatabase references / Derived calculations / Other / Refinement description / Version format compliance

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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-1121
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  • Superimposition on EM map
  • EMDB-1121
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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
Polyers320,7038
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
Polyers19,242,178480
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
Polyers1,603,51540
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
Polyers1,924,21848
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

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Components

#1: Protein/peptide
E1 ENVELOPE GLYCOPROTEIN


Mass: 42554.148 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 810-1248
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Chikungunya / virus
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: 37621.594 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 326-748
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Chikungunya / virus
Strain: 05-115 / Plasmid name: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER / 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 / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sindbis virus / Type: VIRUS
Buffer solutionDetails: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA / 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

MicroscopyMicroscope model: 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 / 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
3D reconstructionResolution: 9 Å / Number 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
Least-squares processHighest resolution: 9 Å
Refine hist #LASTHighest resolution: 9 Å
Number of atoms included #LASTProtein: 22460 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 22460

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