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- PDB-3n40: Crystal structure of the immature envelope glycoprotein complex o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n40 | |||||||||
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Title | Crystal structure of the immature envelope glycoprotein complex of Chikungunya virus. | |||||||||
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![]() | VIRAL PROTEIN / IMMATURE HETERODIMER / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION | |||||||||
Function / homology | ![]() 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 / virion attachment to host cell / host cell plasma membrane / structural molecule activity / 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 / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Voss, J. / Vaney, M.C. / Duquerroy, S. / Rey, F.A. | |||||||||
![]() | ![]() 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: ![]() Title: Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus. Authors: Roussel, A. / Lescar, J. / Vaney, M.C. / Wengler, G. / Rey, F.A. #2: ![]() Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus. Authors: Gibbons, D.L. / Vaney, M.C. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / Rey, F.A. #3: ![]() Title: The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH. Authors: Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Rey, F.A. #4: ![]() Title: Structural Changes of Envelope Proteins During Alphavirus Fusion. Authors: Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.2 KB | Display | ![]() |
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PDB format | ![]() | 267 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xfbC ![]() 2xfcC ![]() 3n41C ![]() 3n42C ![]() 3n43C ![]() 3n44C ![]() 2alaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules PF
#1: Protein | Mass: 45338.363 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 266-666 / Mutation: R325E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 42668.254 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 421 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
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#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: 2.69 Å3/Da / Density % sol: 54.26 % |
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Crystal grow | Temperature: 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 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2009 Details: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Monochromator: (SI 311) OR (SI 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→49.1 Å / Num. obs: 51008 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 37.49 Å2 / Rsym value: 0.085 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.17→2.23 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.424 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: 2ALA Resolution: 2.17→49.1 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→49.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.23 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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