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Yorodumi- EMDB-25471: Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25471 | |||||||||
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Title | Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound | |||||||||
Map data | EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound | |||||||||
Sample |
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Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / membrane => GO:0016020 / extracellular region / Virion spike glycoprotein / Virion spike glycoprotein Function and homology information | |||||||||
Biological species | Homo sapiens (human) / Ebola virus - Gabon (1994-1997) / Zaire ebolavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
Authors | Milligan JC / Yu X / Saphire EO | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2022 Title: Asymmetric and non-stoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses. Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy ...Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy Chennareddy / Arthur J Goff / Ashley E Piper / Sean Hui / Kelly C L Shaffer / Tierra Buck / Megan L Heinrich / Luis M Branco / Ian Crozier / Michael R Holbrook / Jens H Kuhn / Yoshihiro Kawaoka / Pamela J Glass / Alexander Bukreyev / Thomas W Geisbert / Gabriella Worwa / Rafi Ahmed / Erica Ollmann Saphire / Abstract: Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ...Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ebolaviruses. Current cocktails contain antibodies that cross-react with the secreted soluble glycoprotein (sGP) that absorbs virus-neutralizing antibodies. By sorting memory B cells from EBOV infection survivors, we isolated two broadly reactive anti-GP monoclonal antibodies, 1C3 and 1C11, that potently neutralize, protect rodents from disease, and lack sGP cross-reactivity. Both antibodies recognize quaternary epitopes in trimeric ebolavirus GP. 1C11 bridges adjacent protomers via the fusion loop. 1C3 has a tripartite epitope in the center of the trimer apex. One 1C3 antigen-binding fragment anchors simultaneously to the three receptor-binding sites in the GP trimer, and separate 1C3 paratope regions interact differently with identical residues on the three protomers. A cocktail of both antibodies completely protected nonhuman primates from EBOV and SUDV infections, indicating their potential clinical value. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25471.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-25471-v30.xml emd-25471.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_25471.png | 48.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25471 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25471 | HTTPS FTP |
-Related structure data
Related structure data | 7swdMC 7n6pC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25471.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv a...
Entire | Name: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab |
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Components |
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-Supramolecule #1: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv a...
Supramolecule | Name: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Drosophila (fruit flies) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Virion spike glycoprotein GP1
Macromolecule | Name: Virion spike glycoprotein GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus - Gabon (1994-1997) / Strain: Mayinga-76 |
Molecular weight | Theoretical: 31.297158 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR ...String: IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GK LIWKVNP EIDTTIGEWA FWETKKNLTR KIRSEELSFT VVS |
-Macromolecule #2: Virion spike glycoprotein GP2
Macromolecule | Name: Virion spike glycoprotein GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zaire ebolavirus |
Molecular weight | Theoretical: 10.756211 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: IVNAQPKCNP NLHYWTTQDE GAAIGLAWIP YFGPAAEGIY TEGLMHNQDG LICGLRQLAN ETTQALQLFL RATTELRTFS ILNRKAIDF LLQRWGG |
-Macromolecule #3: 1C11 scFv
Macromolecule | Name: 1C11 scFv / 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: 26.783773 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: QVQLVQSGAE VKKPGASVKV SCRTSGYTFS SYNIHWVRQA PGQGLEWMGV INPYGRSTTL YARRFRDRVT MTRDTSTSTV YMELSSLRS EDTAVYFCGR LYSGAPYGLD VWGQGSTVTV SSGTGGSGGG GSGGGGSGGG ASDIVMTQSP LSLPVTPGEP A SISCRSSQ ...String: QVQLVQSGAE VKKPGASVKV SCRTSGYTFS SYNIHWVRQA PGQGLEWMGV INPYGRSTTL YARRFRDRVT MTRDTSTSTV YMELSSLRS EDTAVYFCGR LYSGAPYGLD VWGQGSTVTV SSGTGGSGGG GSGGGGSGGG ASDIVMTQSP LSLPVTPGEP A SISCRSSQ SLLHSNGYNY VDWYLQKPGQ SPQLLIYLGS SRASGVPDRF SGSGSGTDFT LKISRVETED VGIYYCMQGL QT PLTFGGG TKVEIK |
-Macromolecule #4: 1C3 heavy chain
Macromolecule | Name: 1C3 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.308938 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QVQLVQSGAE VKKPGSSVKV ACKVSGGTFS SYTISWVRQA PGQGLEWMGG IIPSFGVGHY SQKFRDRVTL TADKSTTTAF LELSSVRSE DTALYYCAIL GTFNWKSGGN YFGPWGQGTL VTVSS |
-Macromolecule #5: 1C3 light chain
Macromolecule | Name: 1C3 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.62405 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIVLTQSPDS LAASLGERAT ISCKSSHSVL YSSNNKDFFA WYQQKPGQPP KLLISWASTR ESGVPVRFNG GGSGTHFTLT ISSLQAEDV AVYYCQQYFS SPITFGQGTR LEIKRT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Name: TBS |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 54.95 sec. / Average electron dose: 34.97 e/Å2 |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 75948 |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7swd: |