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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22839 | |||||||||
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Title | BDBV-289 bound to EBOV GPdMuc Makona | |||||||||
![]() | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab BDBV-289 | |||||||||
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Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / extracellular region / membrane / Virion spike glycoprotein / Virion spike glycoprotein![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Murin CD / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies. Authors: Charles D Murin / Pavlo Gilchuk / Philipp A Ilinykh / Kai Huang / Natalia Kuzmina / Xiaoli Shen / Jessica F Bruhn / Aubrey L Bryan / Edgar Davidson / Benjamin J Doranz / Lauren E Williamson ...Authors: Charles D Murin / Pavlo Gilchuk / Philipp A Ilinykh / Kai Huang / Natalia Kuzmina / Xiaoli Shen / Jessica F Bruhn / Aubrey L Bryan / Edgar Davidson / Benjamin J Doranz / Lauren E Williamson / Jeffrey Copps / Tanwee Alkutkar / Andrew I Flyak / Alexander Bukreyev / James E Crowe / Andrew B Ward / ![]() Abstract: Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of ...Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies. | |||||||||
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 | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.6 KB 14.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.3 KB | Display | ![]() |
Images | ![]() | 54.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 362.7 KB | Display | ![]() |
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Full document | ![]() | 362.2 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kejMC ![]() 7kewC ![]() 7kexC ![]() 7kf9C ![]() 7kfbC ![]() 7kfeC ![]() 7kfgC ![]() 7kfhC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab BDBV-289 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 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 : Complex of Ebola virus GP (mucin-deleted Makona strain) bound to ...
Entire | Name: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to BDBV-289 Fab |
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Components |
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-Supramolecule #1: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to ...
Supramolecule | Name: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to BDBV-289 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Fab and GP expressed in HEK 293F cells, complexed and purified by size exclusion chromatography |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Virion spike glycoprotein
Macromolecule | Name: Virion spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.978613 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKR WGFRSGVPPK VVNYEAGEWA ENCYNLEIKK PDGSECLPAA PDGIRGFPRC RYVHKVSGTG PCAGDFAFHK E GAFFLYDR ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKR WGFRSGVPPK VVNYEAGEWA ENCYNLEIKK PDGSECLPAA PDGIRGFPRC RYVHKVSGTG PCAGDFAFHK E GAFFLYDR LASTVIYRGT TFAEGVVAFL ILPQAKKDFF SSHPLREPVN ATEDPSSGYY STTIRYQATG FGTNETEYLF EV DNLTYVQ LESRFTPQFL LQLNETIYAS GKRSNTTGKL IWKVNPEIDT TIGEWAFWET KKNLTRKIRS EELSFT |
-Macromolecule #2: Antibody Fab heavy chain (HC) BDBV-289
Macromolecule | Name: Antibody Fab heavy chain (HC) BDBV-289 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.864316 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CKASGATFGS DTVTWVRQAP GQGLEWMGGI IPFFGEANYA QRFQGRVTI TADKSTNTAY MELSSLRSED TAVYFCARQI NEMATFGEIH YYTYMDVWGQ GTLVTVSSAS TKGPSVFPLA P SSKSTSGG ...String: MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CKASGATFGS DTVTWVRQAP GQGLEWMGGI IPFFGEANYA QRFQGRVTI TADKSTNTAY MELSSLRSED TAVYFCARQI NEMATFGEIH YYTYMDVWGQ GTLVTVSSAS TKGPSVFPLA P SSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TK VDKRVEP KSCD |
-Macromolecule #3: Antibody Fab light chain (LC) BDBV-289
Macromolecule | Name: Antibody Fab light chain (LC) BDBV-289 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.725422 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGWSCIILFL VATATGVHGS ELTQDPAVSV ALGQTVRITC QGDSLRNYYA SWYQQKPRQA PVLVFYGKNN RPSGIPDRFS GSSSGNTAS LTISGAQAED EADYYCNSRD SSSNHLVFGG GTKLTVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF Y PGAVTVAW ...String: MGWSCIILFL VATATGVHGS ELTQDPAVSV ALGQTVRITC QGDSLRNYYA SWYQQKPRQA PVLVFYGKNN RPSGIPDRFS GSSSGNTAS LTISGAQAED EADYYCNSRD SSSNHLVFGG GTKLTVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF Y PGAVTVAW KADSSPVKAG VETTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TEC |
-Macromolecule #4: Virion spike glycoprotein
Macromolecule | Name: Virion spike glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.158592 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMH NQDGLICGLR QLANETTQAL QLFLRATTEL RTFSILNRKA IDFLLQRWGG TCHILGPDCC IEPHDWTKNI T DKIDQIIH ...String: NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMH NQDGLICGLR QLANETTQAL QLFLRATTEL RTFSILNRKA IDFLLQRWGG TCHILGPDCC IEPHDWTKNI T DKIDQIIH DDDDKAGWSH PQFEKGGGSG GGSGGGSWSH PQFEK |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |