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Yorodumi- EMDB-22853: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22853 | |||||||||
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Title | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-437 and EBOV-515 | |||||||||
Map data | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-437 and EBOV-515 | |||||||||
Sample |
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Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / extracellular region / membrane / Virion spike glycoprotein / Virion spike glycoprotein Function and homology information | |||||||||
Biological species | Homo sapiens (human) / Ebola virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Murin CD / Ward AB | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell Rep / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22853.map.gz | 8.7 MB | EMDB map data format | |
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Header (meta data) | emd-22853-v30.xml emd-22853.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22853_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_22853.png | 72.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22853 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22853 | HTTPS FTP |
-Validation report
Summary document | emd_22853_validation.pdf.gz | 353.3 KB | Display | EMDB validaton report |
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Full document | emd_22853_full_validation.pdf.gz | 352.8 KB | Display | |
Data in XML | emd_22853_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_22853_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22853 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22853 | HTTPS FTP |
-Related structure data
Related structure data | 7kfhMC 7kejC 7kewC 7kexC 7kf9C 7kfbC 7kfeC 7kfgC 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_22853.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-437 and EBOV-515 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Ebola virus GP (mucin deleted, Makona strain) bound to antibody F...
Entire | Name: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-437 and EBOV-515 |
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Components |
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-Supramolecule #1: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F...
Supramolecule | Name: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-437 and EBOV-515 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: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293F |
-Macromolecule #1: Virion spike glycoprotein 1
Macromolecule | Name: Virion spike glycoprotein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus |
Molecular weight | Theoretical: 34.978613 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 EBOV-437 light chain
Macromolecule | Name: Antibody Fab EBOV-437 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.474068 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QIVLTQSPGT LSLSPGERAT LSCRASQSVS NSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSISRLE PEDFAVYYC QQYGTSPCTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: QIVLTQSPGT LSLSPGERAT LSCRASQSVS NSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSISRLE PEDFAVYYC QQYGTSPCTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLRSPVTK SFNRGEC |
-Macromolecule #3: Virion spike glycoprotein 2
Macromolecule | Name: Virion spike glycoprotein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus |
Molecular weight | Theoretical: 22.158592 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 #4: Antibody Fab EBOV-437 heavy chain
Macromolecule | Name: Antibody Fab EBOV-437 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: 25.268438 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS RDIFSWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADKSTSTVF MELSGLRSE DTAVYFCARG PPLRGERSWF GESEKYDYFY MDVWGKGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS RDIFSWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADKSTSTVF MELSGLRSE DTAVYFCARG PPLRGERSWF GESEKYDYFY MDVWGKGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCD |
-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: 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |