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Yorodumi- PDB-3j2y: Electron Cryo-microscopy of Chikungunya VLP in complex with neutr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j2y | ||||||
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Title | Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab 9.8B | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Alpha virus / Chikungunya VLP / neutralizing antibody 9.8B | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.9 Å | ||||||
Authors | Sun, S. / Xiang, Y. / 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j2y.cif.gz | 327.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j2y.ent.gz | 272.7 KB | Display | PDB format |
PDBx/mmJSON format | 3j2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j2y_validation.pdf.gz | 877.5 KB | Display | wwPDB validaton report |
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Full document | 3j2y_full_validation.pdf.gz | 900 KB | Display | |
Data in XML | 3j2y_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 3j2y_validation.cif.gz | 67.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/3j2y ftp://data.pdbj.org/pub/pdb/validation_reports/j2/3j2y | HTTPS FTP |
-Related structure data
Related structure data | 5578MC 5576C 5577C 5579C 5580C 3j2wC 3j2xC 3j2zC 3j30C 4gq9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Antibody | Mass: 23303.777 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23441.291 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Details of virus | Empty: NO / Enveloped: YES / Host category: INVERTEBRATES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||
Natural host | Organism: Aedes albopictus | ||||||||||||||||
Buffer solution | Name: PBS / pH: 7.4 / Details: PBS | ||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Details: 400 mesh C-flat grids | ||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 90 K / Humidity: 95 % Details: Blot for 2 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3) Method: Blot for 2 seconds before plunging |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/HE / Date: Feb 1, 2011 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 39190 X / Cs: 2 mm Astigmatism: Objective lens astigmatism was corrected at 100000 times magnification Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 |
Image scans | Num. digital images: 100 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each Micrograph | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: projection matching / Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1820 / Actual pixel size: 2.22 Å Details: (Single particle details: The particles were selected using e2boxer) (Single particle--Applied symmetry: I) Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Sumf / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | PDB-ID: 4GQ9 Pdb chain-ID: B | ||||||||||||
Refinement step | Cycle: LAST
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