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Yorodumi- EMDB-8936: Bundibugyo virus GP (mucin-deleted) in complex with pan-ebolaviru... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8936 | |||||||||
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Title | Bundibugyo virus GP (mucin-deleted) in complex with pan-ebolavirus human antibody ADI-15878 Fab | |||||||||
Map data | Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab | |||||||||
Sample |
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Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / viral envelope / extracellular region / membrane / Envelope glycoprotein Function and homology information | |||||||||
Biological species | Ebola virus / Bundibugyo virus / Homo sapiens (human) / Bundibugyo ebolavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.29 Å | |||||||||
Authors | Murin CD / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep / Year: 2018 Title: Structural Basis of Pan-Ebolavirus Neutralization by an Antibody Targeting the Glycoprotein Fusion Loop. Authors: Charles D Murin / Jessica F Bruhn / Zachary A Bornholdt / Jeffrey Copps / Robyn Stanfield / Andrew B Ward / Abstract: Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The ...Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The antibody ADI-15878 was previously identified from a human survivor of Ebola virus Makona variant (EBOV/Mak) infection. This mAb demonstrated potent neutralizing activity against all known ebolaviruses and provided protection in rodent and ferret models against three ebolavirus species. Here, we describe the unliganded crystal structure of ADI-15878 as well as the cryo-EM structures of ADI-15878 in complex with the EBOV/Mak and Bundibugyo virus (BDBV) glycoproteins (GPs). ADI-15878 binds through an induced-fit mechanism by targeting highly conserved residues in the internal fusion loop (IFL), bridging across GP protomers via the heptad repeat 1 (HR1) region. Our structures provide a more complete description of the ebolavirus immunogenic landscape, as well as a molecular basis for how rare but potent antibodies target conserved filoviral fusion machinery. | |||||||||
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_8936.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-8936-v30.xml emd-8936.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8936_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_8936.png | 66.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8936 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8936 | HTTPS FTP |
-Validation report
Summary document | emd_8936_validation.pdf.gz | 340.9 KB | Display | EMDB validaton report |
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Full document | emd_8936_full_validation.pdf.gz | 340.4 KB | Display | |
Data in XML | emd_8936_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_8936_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8936 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8936 | HTTPS FTP |
-Related structure data
Related structure data | 6dzmMC 8935C 6dzlC 6dznC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8936.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 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 : Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to...
Entire | Name: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab |
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Components |
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-Supramolecule #1: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to...
Supramolecule | Name: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Ebola virus |
Molecular weight | Theoretical: 45 KDa |
-Supramolecule #2: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain
Supramolecule | Name: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Bundibugyo virus |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4 |
-Supramolecule #3: Human survivor antibody ADI-15878 Fab
Supramolecule | Name: Human survivor antibody ADI-15878 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 / Details: Fab was generated by papain digestion of IgG |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
-Macromolecule #1: Bundibugyo virus GP1
Macromolecule | Name: Bundibugyo virus GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Bundibugyo ebolavirus |
Molecular weight | Theoretical: 34.697938 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: IPLGVVHNNT LQVSDIDKLV CRDKLSSTSQ LKSVGLNLEG NGVATDVPTA TKRWGFRAGV PPKVVNYEAG EWAENCYNLD IKKADGSEC LPEAPEGVRG FPRCRYVHKV SGTGPCPEGY AFHKEGAFFL YDRLASTIIY RSTTFSEGVV AFLILPETKK D FFQSPPLH ...String: IPLGVVHNNT LQVSDIDKLV CRDKLSSTSQ LKSVGLNLEG NGVATDVPTA TKRWGFRAGV PPKVVNYEAG EWAENCYNLD IKKADGSEC LPEAPEGVRG FPRCRYVHKV SGTGPCPEGY AFHKEGAFFL YDRLASTIIY RSTTFSEGVV AFLILPETKK D FFQSPPLH EPANMTTDPS SYYHTVTLNY VADNFGTNMT NFLFQVDHLT YVQLEPRFTP QFLVQLNETI YTNGRRSNTT GT LIWKVNP TVDTGVGEWA FWENKKNFTK TLSSEELSVI FVPIDISEST EPGPLTNTTR GAANLLTGSR RTRR |
-Macromolecule #2: Bundibugyo virus GP2
Macromolecule | Name: Bundibugyo virus GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Bundibugyo ebolavirus |
Molecular weight | Theoretical: 19.683902 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EITLRTQAKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYTEGIMHNQ NGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF IDKPLPDQTD VEVDDDDKAG WSHPQFEKGG G SGGGSGGG SWSHPQFEK |
-Macromolecule #3: Antibody ADI-15878 Fab, light chain
Macromolecule | Name: Antibody ADI-15878 Fab, light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.333459 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: DIVLTQSPST LSASVGDRVT ITCRASQSIS SWLAWYQQKP GEAPKLLISD ASSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYYSSPTFGG GTKVEIK |
-Macromolecule #4: Antibody ADI-15878 Fab, heavy chain
Macromolecule | Name: Antibody ADI-15878 Fab, heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.043574 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: VQLVQSGVTL VQPGGSLRVS CAASGFTFSS YAMSWVRQAP GKGLEWVSAI SGLGGSTYYA DSVKGRFTIS RDNSKNTLYL QMNSLRAED TAVYYCAKDH RVWAAGYHFD YWGQGALVTV S |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: Solutions were made fresh from 10X concentrate and filtered with a 0.2 micrometer filter into a sterile glass container. | |||||||||
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Details: unspecified | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 3.5s blot on both sides of the grid using Whattman No. 1 filter paper. | |||||||||
Details | Antibody ADI-15878 Fab was added in 10 molar excess to glycoprotein and allowed to incubate overnight at 4 degrees Celsius followed by size exclusion chromatography to purify the complex and rid of excess Fab. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Preliminary grid screening was performed manually |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 38167 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |