+Open data
-Basic information
Entry | Database: PDB / ID: 4gq9 | ||||||
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Title | Chikungunya virus neutralizing antibody 9.8B Fab fragment | ||||||
Components |
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Keywords | VIRAL PROTEIN / IgG fold / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å | ||||||
Authors | Sun, S. / Rossmann, M.G. | ||||||
Citation | Journal: Elife / Year: 2013 Title: Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization. Authors: Siyang Sun / Ye Xiang / Wataru Akahata / Heather Holdaway / Pankaj Pal / Xinzheng Zhang / Michael S Diamond / Gary J Nabel / Michael G Rossmann / Abstract: A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 ...A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gq9.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gq9.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/4gq9 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gq9 | HTTPS FTP |
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-Related structure data
Related structure data | 5576C 5577C 5578C 5579C 5580C 3j2wC 3j2xC 3j2yC 3j2zC 3j30C 3dggS S: Starting model for refinement 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
#1: Antibody | Mass: 23303.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23441.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 0.1M Tris-Cl pH 8.5 and 0.2M lithium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96801 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2010 / Details: mirrors |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96801 Å / Relative weight: 1 |
Reflection | Resolution: 2.995→50 Å / Num. all: 11921 / Num. obs: 11714 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 62.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.995→3.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4.3 / Num. unique all: 590 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DGG Resolution: 2.995→43.42 Å / Cor.coef. Fo:Fc: 0.803 / Cor.coef. Fo:Fc free: 0.726 / SU B: 92.327 / SU ML: 0.749 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.987 Å2
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Refinement step | Cycle: LAST / Resolution: 2.995→43.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.995→3.073 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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