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Yorodumi- EMDB-8935: Ebola virus Makona variant GP (mucin-deleted) in complex with pan... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8935 | |||||||||
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Title | Ebola virus Makona variant GP (mucin-deleted) in complex with pan-ebolavirus human antibody ADI-15878 Fab | |||||||||
Map data | Ebola virus glycoprotein (mucin-deleted) Makona variant ectodomain bound to human survivor antibody ADI-15878 Fab. | |||||||||
Sample |
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Function / homology | Function and homology information clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane ...clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Ebola virus / Homo sa (virus) / Zaire ebolavirus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.14 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_8935.map.gz | 13.5 MB | EMDB map data format | |
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Header (meta data) | emd-8935-v30.xml emd-8935.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8935_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_8935.png | 59 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8935 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8935 | HTTPS FTP |
-Validation report
Summary document | emd_8935_validation.pdf.gz | 334.8 KB | Display | EMDB validaton report |
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Full document | emd_8935_full_validation.pdf.gz | 334.4 KB | Display | |
Data in XML | emd_8935_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_8935_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8935 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8935 | HTTPS FTP |
-Related structure data
Related structure data | 6dzlMC 8936C 6dzmC 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_8935.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ebola virus glycoprotein (mucin-deleted) Makona variant ectodomain bound to human survivor antibody ADI-15878 Fab. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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 : Ebola virus Zaire (Makona variant) glycoprotein (mucin-deleted) e...
Entire | Name: Ebola virus Zaire (Makona variant) glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab |
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Components |
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-Supramolecule #1: Ebola virus Zaire (Makona variant) glycoprotein (mucin-deleted) e...
Supramolecule | Name: Ebola virus Zaire (Makona variant) glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4 |
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Source (natural) | Organism: Ebola virus |
Molecular weight | Theoretical: 45 KDa |
-Supramolecule #2: Ebola virus Zaire (Makona variant) glycoprotein (mucin-deleted) e...
Supramolecule | Name: Ebola virus Zaire (Makona variant) glycoprotein (mucin-deleted) ectodomain type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Ebola 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 sa (virus) |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
-Macromolecule #1: Ebola virus Makona GP1
Macromolecule | Name: Ebola virus Makona GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zaire ebolavirus / Strain: Kikwit-95 |
Molecular weight | Theoretical: 35.51775 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SIPLGVIHNS TLQVSDVDKL VCRDKLSSTN QLRSVGLNLE GNGVATDVPS VTKRWGFRSG VPPKVVNYEA GEWAENCYNL EIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK K DFFSSHPL ...String: SIPLGVIHNS TLQVSDVDKL VCRDKLSSTN QLRSVGLNLE GNGVATDVPS VTKRWGFRSG VPPKVVNYEA GEWAENCYNL EIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK K DFFSSHPL REPVNATEDP SSGYYSTTIR YQATGFGTNE TEYLFEVDNL TYVQLESRFT PQFLLQLNET IYASGKRSNT TG KLIWKVN PEIDTTIGEW AFWETKKNLT RKIRSEELSF TAVNNNTHHQ DTGEESASSG KLGLITNTIA GVAGLITGGR RTR R |
-Macromolecule #2: Ebola virus Makona GP2
Macromolecule | Name: Ebola virus Makona GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zaire ebolavirus / Strain: Kikwit-95 |
Molecular weight | Theoretical: 18.334406 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVIVNAQPKC NPNLHFWTTQ DEGAAIGLAW IPYFGPAAEG IYTEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDV EVDDDDKAGW SHPQFEKGGG SGGGSGGGSW S HPQFEK |
-Macromolecule #3: Fv domain of ADI-15878 Fab light chain
Macromolecule | Name: Fv domain of 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: Fv domain of ADI-15878 Fab heavy chain
Macromolecule | Name: Fv domain of 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: 13.171703 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: QVQLVQSGVT LVQPGGSLRV SCAASGFTFS SYAMSWVRQA PGKGLEWVSA ISGLGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKD HRVWAAGYHF DYWGQGALVT VS |
-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 | Model: C-flat-1.2/1.3 4C / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER | |||||||||
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 TALOS ARCTICA |
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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: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 43478 / 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: Talos Arctica / Image courtesy: FEI Company |