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Yorodumi- EMDB-22852: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22852 | |||||||||
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Title | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 and EBOV-515 | |||||||||
Map data | Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 and EBOV-515 | |||||||||
Sample |
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Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / membrane => GO:0016020 / viral envelope / extracellular region / membrane / Spike glycoprotein / Envelope glycoprotein Function and homology information | |||||||||
Biological species | Ebola virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.9 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_22852.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-22852-v30.xml emd-22852.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22852_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_22852.png | 46.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22852 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22852 | HTTPS FTP |
-Validation report
Summary document | emd_22852_validation.pdf.gz | 326.2 KB | Display | EMDB validaton report |
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Full document | emd_22852_full_validation.pdf.gz | 325.7 KB | Display | |
Data in XML | emd_22852_validation.xml.gz | 11.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22852 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22852 | HTTPS FTP |
-Related structure data
Related structure data | 7kejC 7kewC 7kexC 7kf9C 7kfbC 7kfeC 7kfgC 7kfhC 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_22852.map.gz / Format: CCP4 / Size: 91.1 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-237 and EBOV-515 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 GP (mucin deleted, Makona strain) bound to antibody F...
Entire | Name: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 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-237 and EBOV-515 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Parts of complex expressed and purified recombinantly, complexed and purified by gel filtration |
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Source (natural) | Organism: Ebola virus |
-Supramolecule #2: Antibody Fab EBOV-237
Supramolecule | Name: Antibody Fab EBOV-237 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Ebola virus GP (mucin deleted, Makona strain)
Supramolecule | Name: Ebola virus GP (mucin deleted, Makona strain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Ebola virus |
-Macromolecule #1: Ebola virus GP1 (mucin deleted, Makona strain)
Macromolecule | Name: Ebola virus GP1 (mucin deleted, Makona strain) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKRW GFRSGVPPKV VNYEAGEWAE NCYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKRW GFRSGVPPKV VNYEAGEWAE NCYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA STVIYRGTTF AEGVVAFLIL PQAKKDFFSS HPLREPVNAT EDPSSGYYST TIRYQATGFG TNETEYLFEV DNLTYVQLES RFTPQFLLQL NETIYASGKR SNTTGKLIWK VNPEIDTTIG EWAFWETKKN LTRKIRSEEL SFT |
-Macromolecule #2: Ebola virus GP2 (Makona strain)
Macromolecule | Name: Ebola virus GP2 (Makona strain) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDD ...String: NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDD DDKAGWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK |
-Macromolecule #3: Antibody Fab EBOV-237 heavy chain
Macromolecule | Name: Antibody Fab EBOV-237 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSGTLSL TCAVSGGSIS NGIWWSWVRQ PPGKGLEWIG EIYHSGSTNY SPSLKSRVTI SLDKSKNQFS LKLNSVTAAD TAVYYCARAP SQFDFSDWLV PQGAMFRGHY IDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP ...String: QVQLQESGPG LVKPSGTLSL TCAVSGGSIS NGIWWSWVRQ PPGKGLEWIG EIYHSGSTNY SPSLKSRVTI SLDKSKNQFS LKLNSVTAAD TAVYYCARAP SQFDFSDWLV PQGAMFRGHY IDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCD |
-Macromolecule #4: Antibody Fab EBOV-237 light chain
Macromolecule | Name: Antibody Fab EBOV-237 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIVMTQSPDS LAVSLGERAT INCKSSQSVL YNSNNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLA ISSLRAEDVA VYYCQQYYSA PYTFGQGTKM EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT ...String: DIVMTQSPDS LAVSLGERAT INCKSSQSVL YNSNNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLA ISSLRAEDVA VYYCQQYYSA PYTFGQGTKM EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC |
-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 TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |