[English] 日本語
Yorodumi- EMDB-6235: Negative stain single particle electron microscopy of Marburg Vir... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6235 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Negative stain single particle electron microscopy of Marburg Virus Glycoproteins bound to antibodies from a human survivor | |||||||||
Map data | Reconstruction of Marburg Virus GP bound to antibody MR82 from a human survivor | |||||||||
Sample |
| |||||||||
Keywords | Marburg Virus / Antibodies / Neutralization / Glycoprotein | |||||||||
Biological species | Marburg marburgvirus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Flyak A / Ilinykh PA / Murin CD / Garron T / Shen X / Fusco ML / Hashiguchi T / Bornholdt ZA / Slaughter C / Sapparapu G ...Flyak A / Ilinykh PA / Murin CD / Garron T / Shen X / Fusco ML / Hashiguchi T / Bornholdt ZA / Slaughter C / Sapparapu G / Ksiazek TG / Ward AB / Saphire EO / Bukreyev A / Crowe JE | |||||||||
Citation | Journal: Cell / Year: 2015 Title: Mechanism of human antibody-mediated neutralization of Marburg virus. Authors: Andrew I Flyak / Philipp A Ilinykh / Charles D Murin / Tania Garron / Xiaoli Shen / Marnie L Fusco / Takao Hashiguchi / Zachary A Bornholdt / James C Slaughter / Gopal Sapparapu / Curtis ...Authors: Andrew I Flyak / Philipp A Ilinykh / Charles D Murin / Tania Garron / Xiaoli Shen / Marnie L Fusco / Takao Hashiguchi / Zachary A Bornholdt / James C Slaughter / Gopal Sapparapu / Curtis Klages / Thomas G Ksiazek / Andrew B Ward / Erica Ollmann Saphire / Alexander Bukreyev / James E Crowe / Abstract: The mechanisms by which neutralizing antibodies inhibit Marburg virus (MARV) are not known. We isolated a panel of neutralizing antibodies from a human MARV survivor that bind to MARV glycoprotein ...The mechanisms by which neutralizing antibodies inhibit Marburg virus (MARV) are not known. We isolated a panel of neutralizing antibodies from a human MARV survivor that bind to MARV glycoprotein (GP) and compete for binding to a single major antigenic site. Remarkably, several of the antibodies also bind to Ebola virus (EBOV) GP. Single-particle EM structures of antibody-GP complexes reveal that all of the neutralizing antibodies bind to MARV GP at or near the predicted region of the receptor-binding site. The presence of the glycan cap or mucin-like domain blocks binding of neutralizing antibodies to EBOV GP, but not to MARV GP. The data suggest that MARV-neutralizing antibodies inhibit virus by binding to infectious virions at the exposed MARV receptor-binding site, revealing a mechanism of filovirus inhibition. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6235.map.gz | 2.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6235-v30.xml emd-6235.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_6235.jpg | 585.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6235 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6235 | HTTPS FTP |
-Validation report
Summary document | emd_6235_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6235_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_6235_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6235 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6235 | HTTPS FTP |
-Related structure data
Related structure data | 6232C 6233C 6234C 6236C 6237C 6238C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6235.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of Marburg Virus GP bound to antibody MR82 from a human survivor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Fab Fragment of MR82 human IgG1 monoclonal antibody to Marburg Vi...
Entire | Name: Fab Fragment of MR82 human IgG1 monoclonal antibody to Marburg Virus GP |
---|---|
Components |
|
-Supramolecule #1000: Fab Fragment of MR82 human IgG1 monoclonal antibody to Marburg Vi...
Supramolecule | Name: Fab Fragment of MR82 human IgG1 monoclonal antibody to Marburg Virus GP type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 2 |
---|---|
Molecular weight | Theoretical: 310 KDa |
-Macromolecule #1: GP, mucin-deleted
Macromolecule | Name: GP, mucin-deleted / type: protein_or_peptide / ID: 1 / Name.synonym: glycoprotein Details: Recombinant Marburg Virus GP; mucin-like domains were not included in the construct. Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Marburg marburgvirus / synonym: Marburg virus |
Molecular weight | Theoretical: 160 MDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) / Recombinant cell: Schneider S2 cells / Recombinant plasmid: pMT-puro |
-Macromolecule #2: Human Monoclonal Antibody IgG1
Macromolecule | Name: Human Monoclonal Antibody IgG1 / type: protein_or_peptide / ID: 2 / Name.synonym: IgG1, monoclonal mAb / Details: Human monoclonal antibody IgG1, MR82 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Peripheral blood mononuclear cells |
Molecular weight | Theoretical: 150 KDa |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 20 mM Tris, 150 mM NaCl |
Staining | Type: NEGATIVE Details: Grids with absorbed protein stained with 2% uranyl formate for 30 seconds |
Grid | Details: 400 mesh copper grid with carbon support, plasma cleaned 20 seconds (Ar/O2 mix, Gatan) |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
---|---|
Date | Nov 12, 2013 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 166 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected using DoG picker. |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 2554 |