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Yorodumi- PDB-3n44: Crystal structure of the mature envelope glycoprotein complex (tr... -
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-Basic information
Entry | Database: PDB / ID: 3n44 | ||||||
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Title | Crystal structure of the mature envelope glycoprotein complex (trypsin cleavage; Osmium soak) of Chikungunya virus. | ||||||
Components |
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Keywords | VIRAL PROTEIN / IMMATURE HETERODIMER / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION | ||||||
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 / 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 | Chikungunya virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Voss, J. / 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: 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: Journal: Nature / Year: 2004 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: 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. Authors: Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Rey, F.A. #4: Journal: To be Published Title: Structural Changes of Envelope Proteins During Alphavirus Fusion. Authors: Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n44.cif.gz | 328 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n44.ent.gz | 264.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n44_validation.pdf.gz | 485.3 KB | Display | wwPDB validaton report |
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Full document | 3n44_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 3n44_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 3n44_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n44 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n44 | HTTPS FTP |
-Related structure data
Related structure data | 2xfbC 2xfcC 3n40C 3n41C 3n42C 3n43C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABF
#1: Protein | Mass: 7470.737 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 266-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5 |
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#2: Protein | Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 329-666 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5 |
#3: Protein | Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1200 / Mutation: P1046A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5 |
-Sugars , 1 types, 2 molecules
#5: Sugar |
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-Non-polymers , 3 types, 277 molecules
#4: Chemical | #6: Chemical | ChemComp-OS / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.74 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.14 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2009 Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→80 Å / Num. obs: 35477 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 48.83 Å2 / Rsym value: 0.051 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.255 / % possible all: 62.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: P62E1 ENVELOPE GLYCOPROTEINS FROM CHIKUNGUNYA VIRUS Resolution: 2.35→48.3 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.877 / SU R Cruickshank DPI: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 51.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→48.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.42 Å / Total num. of bins used: 18
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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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