+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6466 | |||||||||
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Title | Cryo-EM of CHIKV VLP | |||||||||
Map data | Reconstruction of CHIKV virus-like particle | |||||||||
Sample |
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Keywords | chikungunya / cryo-EM | |||||||||
Biological species | Chikungunya virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.3 Å | |||||||||
Authors | Jin J / Liss N / Chen D-H / Liao M / Fox JM / Shimak RM / Fong RH / Chafets D / Bakkour S / Keating S ...Jin J / Liss N / Chen D-H / Liao M / Fox JM / Shimak RM / Fong RH / Chafets D / Bakkour S / Keating S / Fomin ME / Muench MO / Sherman MB / Doranz BJ / Diamond MS / Simmons G | |||||||||
Citation | Journal: Cell Rep / Year: 2015 Title: Neutralizing Monoclonal Antibodies Block Chikungunya Virus Entry and Release by Targeting an Epitope Critical to Viral Pathogenesis. Authors: Jing Jin / Nathan M Liss / Dong-Hua Chen / Maofu Liao / Julie M Fox / Raeann M Shimak / Rachel H Fong / Daniel Chafets / Sonia Bakkour / Sheila Keating / Marina E Fomin / Marcus O Muench / ...Authors: Jing Jin / Nathan M Liss / Dong-Hua Chen / Maofu Liao / Julie M Fox / Raeann M Shimak / Rachel H Fong / Daniel Chafets / Sonia Bakkour / Sheila Keating / Marina E Fomin / Marcus O Muench / Michael B Sherman / Benjamin J Doranz / Michael S Diamond / Graham Simmons / Abstract: We evaluated the mechanism by which neutralizing human monoclonal antibodies inhibit chikungunya virus (CHIKV) infection. Potently neutralizing antibodies (NAbs) blocked infection at multiple steps ...We evaluated the mechanism by which neutralizing human monoclonal antibodies inhibit chikungunya virus (CHIKV) infection. Potently neutralizing antibodies (NAbs) blocked infection at multiple steps of the virus life cycle, including entry and release. Cryo-electron microscopy structures of Fab fragments of two human NAbs and chikungunya virus-like particles showed a binding footprint that spanned independent domains on neighboring E2 subunits within one viral spike, suggesting a mechanism for inhibiting low-pH-dependent membrane fusion. Detailed epitope mapping identified amino acid E2-W64 as a critical interaction residue. An escape mutation (E2-W64G) at this residue rendered CHIKV attenuated in mice. Consistent with these data, CHIKV-E2-W64G failed to emerge in vivo under the selection pressure of one of the NAbs, IM-CKV063. As our study suggests that antibodies engaging the residue E2-W64 can potently inhibit CHIKV at multiple stages of infection, antibody-based therapies or immunogens that target this region might have protective value. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6466.map.gz | 140.6 MB | EMDB map data format | |
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Header (meta data) | emd-6466-v30.xml emd-6466.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | 400_6466.gif 80_6466.gif | 29.1 KB 2.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6466 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6466 | HTTPS FTP |
-Validation report
Summary document | emd_6466_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_6466_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_6466_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6466 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6466 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6466.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of CHIKV virus-like particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Virus-like particle of Chikungunya virus (S27)
Entire | Name: Virus-like particle of Chikungunya virus (S27) |
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Components |
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-Supramolecule #1000: Virus-like particle of Chikungunya virus (S27)
Supramolecule | Name: Virus-like particle of Chikungunya virus (S27) / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Chikungunya virus
Supramolecule | Name: Chikungunya virus / type: virus / ID: 1 / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: S27 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 680 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl |
Grid | Details: Quantifoil copper grids (R2/1, 200 mesh) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2.5 seconds before plunging. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification. |
Date | Sep 25, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Digitization - Sampling interval: 15.6 µm / Number real images: 350 / Average electron dose: 18 e/Å2 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particle images were automatically boxed out using the program ethan. |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.3 Å / Resolution method: OTHER / Software - Name: Relion_1.3 / Number images used: 5510 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: B / Chain - #1 - Chain ID: C / Chain - #2 - Chain ID: D / Chain - #3 - Chain ID: N / Chain - #4 - Chain ID: O / Chain - #5 - Chain ID: P |
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Software | Name: Chimera |
Details | The fitting was done manually first, then with "Fit in Map" in Chimera. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |