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

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Entry
Database: PDB / ID: 2xfb
TitleCHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SINDBIS VIRUS cryo- EM MAP
DescriptorE1 ENVELOPE GLYCOPROTEIN
E2 ENVELOPE GLYCOPROTEIN
KeywordsVIRUS / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION / ICOSAHEDRAL ENVELOPED VIRUS
Specimen sourceCHIKUNGUNYA VIRUS / virus
MethodElectron microscopy (9 Å resolution / Particle / Single particle)
AuthorsVoss, J.E. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
CitationNature, 2010, 468, 709-712

primary. Nature, 2010, 468, 709-712 Yorodumi Papers
Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
James E Voss / Marie-Christine Vaney / Stéphane Duquerroy / Clemens Vonrhein / Christine Girard-Blanc / Elodie Crublet / Andrew Thompson / Gérard Bricogne / Félix A Rey

#1. Structure, 2006, 14, 63- Yorodumi Papers
Mapping the Structure and Function of the E1 and E2 Glycoproteins in Alphaviruses.
Mukhopadhyay, S. / Zhang, W. / Gabler, S. / Chipman, P.R. / Strauss, E.G. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.

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

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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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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: Polypeptide(L)
E1 ENVELOPE GLYCOPROTEIN


Mass: 42554.148 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 810-1248 / Source: (gene. exp.) CHIKUNGUNYA VIRUS / virus / References: UniProt: Q1H8W5

Cellular component

Molecular function

Biological process

  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)
#2: Polypeptide(L)
E2 ENVELOPE GLYCOPROTEIN


Mass: 37621.594 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 326-748 / Source: (gene. exp.) CHIKUNGUNYA VIRUS / virus / References: UniProt: Q1H8W5

Cellular component

Molecular function

Biological process

  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)

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Experimental details

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Experiment

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

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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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