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Yorodumi- EMDB-3149: Electron cryo-microscopy of chikungunya virus in complex with neu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3149 | |||||||||
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Title | Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab 5M16 | |||||||||
Map data | Reconstruction of CHIKV VLP in complex of Fab molecules | |||||||||
Sample |
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Keywords | chikungunya virus / neutralizing antibody Fab | |||||||||
Biological species | Homo sapiens (human) / Chikungunya virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.8 Å | |||||||||
Authors | Long F / Fong RH / Austin SK / Chen Z / Klose T / Fokine A / Liu Y / Porta J / Sapparapu G / Akahata W ...Long F / Fong RH / Austin SK / Chen Z / Klose T / Fokine A / Liu Y / Porta J / Sapparapu G / Akahata W / Doranz BJ / Crowe JE / Diamond MS / Rossmann MG | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity. Authors: Feng Long / Rachel H Fong / Stephen K Austin / Zhenguo Chen / Thomas Klose / Andrei Fokine / Yue Liu / Jason Porta / Gopal Sapparapu / Wataru Akahata / Benjamin J Doranz / James E Crowe / ...Authors: Feng Long / Rachel H Fong / Stephen K Austin / Zhenguo Chen / Thomas Klose / Andrei Fokine / Yue Liu / Jason Porta / Gopal Sapparapu / Wataru Akahata / Benjamin J Doranz / James E Crowe / Michael S Diamond / Michael G Rossmann / Abstract: Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have ...Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain's β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes. | |||||||||
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_3149.map.gz | 427.3 MB | EMDB map data format | |
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Header (meta data) | emd-3149-v30.xml emd-3149.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd-3149-5M16_500by500.tif | 1.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3149 | HTTPS FTP |
-Validation report
Summary document | emd_3149_validation.pdf.gz | 254.4 KB | Display | EMDB validaton report |
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Full document | emd_3149_full_validation.pdf.gz | 253.5 KB | Display | |
Data in XML | emd_3149_validation.xml.gz | 8.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3149 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3149 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3149.map.gz / Format: CCP4 / Size: 523.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of CHIKV VLP in complex of Fab molecules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.39 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 : Electron Cryo-microscopy of Chikungunya VLP in complex with human...
Entire | Name: Electron Cryo-microscopy of Chikungunya VLP in complex with human neutralizing antibody Fab 5M16 |
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Components |
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-Supramolecule #1000: Electron Cryo-microscopy of Chikungunya VLP in complex with human...
Supramolecule | Name: Electron Cryo-microscopy of Chikungunya VLP in complex with human neutralizing antibody Fab 5M16 type: sample / ID: 1000 Oligomeric state: one Fab binds to one envelope protein on the surface of virus Number unique components: 2 |
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-Supramolecule #1: Chikungunya virus
Supramolecule | Name: Chikungunya virus / type: virus / ID: 1 / Name.synonym: Chikungunya VLP / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: strain 37997 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Chikungunya VLP |
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Host (natural) | Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES |
Host system | Organism: Homo sapiens (human) / Recombinant cell: FreeStyle 293-F |
Virus shell | Shell ID: 1 / Diameter: 700 Å / T number (triangulation number): 4 |
-Macromolecule #1: Fab 5M16
Macromolecule | Name: Fab 5M16 / type: protein_or_peptide / ID: 1 / Number of copies: 240 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: hybridoma |
Molecular weight | Experimental: 50 KDa / Theoretical: 50 KDa |
-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: 7.2 / Details: PBS |
Grid | Details: 400 mesh ultrathin holey carbon copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 110 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 6 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Jul 19, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 120 / Average electron dose: 22 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 60553 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were mannually selected using the program EMAN2. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.8 Å / Resolution method: OTHER / Software - Name: JSPR / Number images used: 3090 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: EMFit |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |