[English] 日本語
Yorodumi- EMDB-6368: Electron Cryo-microscopy of Chikungunya virus-like particles in c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6368 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Electron Cryo-microscopy of Chikungunya virus-like particles in complex with neutralizing antibody Fab 8B10 | |||||||||
Map data | Single-particle reconstruction of CHIK-VLP:Fab 8B10 | |||||||||
Sample |
| |||||||||
Keywords | antibody neutralization / Chikungunya / Fab | |||||||||
Biological species | Mus musculus (house mouse) / Chikungunya virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.6 Å | |||||||||
Authors | Porta JC / Mangala Prasad V / Wang CI / Akahata W / Ng LFP / Rossmann MG | |||||||||
Citation | Journal: J Virol / Year: 2016 Title: Structural Studies of Chikungunya Virus-Like Particles Complexed with Human Antibodies: Neutralization and Cell-to-Cell Transmission. Authors: Jason Porta / Vidya Mangala Prasad / Cheng-I Wang / Wataru Akahata / Lisa F P Ng / Michael G Rossmann / Abstract: Chikungunya virus is a positive-stranded RNA alphavirus. Structures of chikungunya virus-like particles in complex with strongly neutralizing antibody Fab fragments (8B10 and 5F10) were determined ...Chikungunya virus is a positive-stranded RNA alphavirus. Structures of chikungunya virus-like particles in complex with strongly neutralizing antibody Fab fragments (8B10 and 5F10) were determined using cryo-electron microscopy and X-ray crystallography. By fitting the crystallographically determined structures of these Fab fragments into the cryo-electron density maps, we show that Fab fragments of antibody 8B10 extend radially from the viral surface and block receptor binding on the E2 glycoprotein. In contrast, Fab fragments of antibody 5F10 bind the tip of the E2 B domain and lie tangentially on the viral surface. Fab 5F10 fixes the B domain rigidly to the surface of the virus, blocking exposure of the fusion loop on glycoprotein E1 and therefore preventing the virus from becoming fusogenic. Although Fab 5F10 can neutralize the wild-type virus, it can also bind to a mutant virus without inhibiting fusion or attachment. Although the mutant virus is no longer able to propagate by extracellular budding, it can, however, enter the next cell by traveling through junctional complexes without being intercepted by a neutralizing antibody to the wild-type virus, thus clarifying how cell-to-cell transmission can occur. IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Chikungunya virus (CHIKV), which belongs to the Alphavirus genus, has a wide distribution in the Old World that has expanded in ...IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Chikungunya virus (CHIKV), which belongs to the Alphavirus genus, has a wide distribution in the Old World that has expanded in recent years into the Americas. There are currently no vaccines or drugs against alphaviral infections. Therefore, a better understanding of CHIKV and its associated neutralizing antibodies will aid in the development of effective treatments. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6368.map.gz | 49.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6368-v30.xml emd-6368.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_6368.png | 134.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6368 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6368 | HTTPS FTP |
-Validation report
Summary document | emd_6368_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6368_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_6368_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6368 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6368 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6368.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Single-particle reconstruction of CHIK-VLP:Fab 8B10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Fab fragment of human antibody 8B10 bound to Chikungunya virus
Entire | Name: Fab fragment of human antibody 8B10 bound to Chikungunya virus |
---|---|
Components |
|
-Supramolecule #1000: Fab fragment of human antibody 8B10 bound to Chikungunya virus
Supramolecule | Name: Fab fragment of human antibody 8B10 bound to Chikungunya virus type: sample / ID: 1000 / Number unique components: 2 |
---|---|
Molecular weight | Experimental: 5.25 MDa / Method: Sedimentation |
-Supramolecule #1: Chikungunya virus
Supramolecule | Name: Chikungunya virus / type: virus / ID: 1 / Name.synonym: CHIK-VLP / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: LR2006 OPY-1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes / Syn species name: CHIK-VLP |
---|---|
Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Host system | Organism: Cricetinae (hamsters) / Recombinant strain: LR2006 OPY-1 / Recombinant cell: BHK-15 / Recombinant plasmid: E37997, Eopy-1 |
Molecular weight | Experimental: 5.25 MDa |
Virus shell | Shell ID: 1 / Name: E1E2 / Diameter: 700 Å / T number (triangulation number): 4 |
-Macromolecule #1: neutralizing antibody Fab 8B10
Macromolecule | Name: neutralizing antibody Fab 8B10 / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / synonym: mouse |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 7.6 / Details: PBS |
Grid | Details: 400 mesh Cu holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 80 K / Max: 100 K / Average: 95 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification. |
Specialist optics | Energy filter - Name: FEI |
Date | May 24, 2014 |
Image recording | Category: CCD / Film or detector model: FEI CETA (4k x 4k) / Digitization - Sampling interval: 2.5 µm / Number real images: 96 / Average electron dose: 22 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 60521 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.35 µm / Nominal defocus min: 0.185 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Nitrogen-cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Manual selection using e2boxer software |
---|---|
CTF correction | Details: Each image |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.6 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 1582 |
Final two d classification | Number classes: 10 |