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- PDB-3n43: Crystal structures of the mature envelope glycoprotein complex (t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n43 | ||||||||||||||||||
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Title | Crystal structures of the mature envelope glycoprotein complex (trypsin cleavage) of Chikungunya virus. | ||||||||||||||||||
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Function / homology | Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set ...Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Alphavirus E1 glycoprotein / ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Specimen source | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Voss, J. / Vaney, M.C. / Duquerroy, S. / Rey, F.A. | ||||||||||||||||||
![]() | Journal: Nature / Year: 2010 Title: Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. ![]() #1: Journal: Structure / Year: 2006 Title: Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus. ![]() #2: Journal: Nature / Year: 2004 Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus. ![]() #3: Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH. ![]() #4: Journal: To be Published Title: Structural Changes of Envelope Proteins During Alphavirus Fusion. ![]() | ||||||||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||||||||
Date | Deposition: May 21, 2010 / Release: Dec 1, 2010
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmcif format | ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
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Links
-Related structure data
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell | γ α β
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Components
-Protein/peptide , 3 types, 3 molecules ABF
#1: Protein/peptide | Mass: 7470.737 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 268-318 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 332-667 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1200 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 157 molecules 






#4: Chemical | #5: Chemical | ChemComp-NDG / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE RESIDUES ARE PART OF THE LINKER BETWEEN P AND F CHAINS. LINKER WAS CLEAVED BY CHYMOTRYPSIN ...THE RESIDUES ARE PART OF THE LINKER BETWEEN P AND F CHAINS. LINKER WAS CLEAVED BY CHYMOTRYPS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 / Density percent sol: 49.12 % |
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Crystal grow![]() | Temp: 293 K / pH: 7 Details: 8-12% PEG4K, 100mM NaAcetate, 100mM Hepes pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 kelvins |
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Source | Source: ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY Detector: CCD / Collection date: Sep 19, 2009 |
Radiation | Monochromator: SI(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | B iso Wilson estimate: 47.71 Å2 / D resolution high: 2.58 Å / D resolution low: 89.72 Å / Observed criterion sigma I: 0 / Rsym value: 0.129 / NetI over sigmaI: 8.8 / Redundancy: 3.9 % / Percent possible obs: 97.7 |
Reflection shell | Highest resolution: 2.6 Å / Lowest resolution: 2.73 Å / MeanI over sigI obs: 2 / Rsym value: 0.31 / Redundancy: 2 % / Percent possible all: 93.1 |
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Processing
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Refine | Method to determine structure![]() ![]() Starting model: P62E1 ENVELOPE GLYCOPROTEINS FROM CHIKUNGUNYA VIRUS Correlation coeff Fo to Fc: 0.867 / Correlation coeff Fo to Fc free: 0.862 / Overall SU R Cruickshank DPI: 0.693 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | B iso mean: 45.49 Å2 / Aniso B11: 0.5439 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 11.5921 Å2 / Aniso B23: 0 Å2 / Aniso B33: -12.136 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Least-squares process | R factor R free![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.48 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine hist #LAST | Highest resolution: 2.58 Å / Lowest resolution: 44 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Number of atoms included #LAST | Protein: 6039 / Nucleic acid: 0 / Ligand: 46 / Solvent: 153 / Total: 6238 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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