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- EMDB-6232: Negative stain single particle electron microscopy of Marburg Vir... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6232 | |||||||||
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Title | Negative stain single particle electron microscopy of Marburg Virus Glycoproteins bound to antibodies from a human survivor | |||||||||
![]() | Reconstruction of Marburg Virus GP bound to Fab MR72 | |||||||||
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![]() | Marburg Virus / Antibodies / Neutralization / Glycoprotein | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 27.0 Å | |||||||||
![]() | 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 | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
Images | ![]() | 544.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.9 KB | Display | ![]() |
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Full document | ![]() | 78.1 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6233C ![]() 6234C ![]() 6235C ![]() 6236C ![]() 6237C ![]() 6238C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of Marburg Virus GP bound to Fab MR72 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Fab Fragment of MR72 human IgG1 monoclonal antibody to Marburg Vi...
Entire | Name: Fab Fragment of MR72 human IgG1 monoclonal antibody to Marburg Virus GP |
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Components |
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-Supramolecule #1000: Fab Fragment of MR72 human IgG1 monoclonal antibody to Marburg Vi...
Supramolecule | Name: Fab Fragment of MR72 human IgG1 monoclonal antibody to Marburg Virus GP type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 2 |
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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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 160 MDa |
Recombinant expression | Organism: ![]() ![]() |
-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, MR72 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 150 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.03 mg/mL |
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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 |
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Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Date | Nov 12, 2013 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 200 |
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 |
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Image processing
Details | Particles were selected using DoG picker. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 978 |