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Yorodumi- EMDB-28190: SARS-CoV-2 RBD in complex with biparatopic nanobody BP10 local re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28190 | |||||||||
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Title | SARS-CoV-2 RBD in complex with biparatopic nanobody BP10 local refinement | |||||||||
Map data | SARS-CoV-2 RBD in complex with biparatopic nanobody BP10 local refinement | |||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
Authors | Pymm PG / Glukhova A / Tham WH | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: iScience / Year: 2022 Title: Biparatopic nanobodies targeting the receptor binding domain efficiently neutralize SARS-CoV-2. Authors: Phillip Pymm / Samuel J Redmond / Olan Dolezal / Francesca Mordant / Ester Lopez / James P Cooney / Kathryn C Davidson / Ebene R Haycroft / Chee Wah Tan / Rebecca Seneviratna / Samantha L ...Authors: Phillip Pymm / Samuel J Redmond / Olan Dolezal / Francesca Mordant / Ester Lopez / James P Cooney / Kathryn C Davidson / Ebene R Haycroft / Chee Wah Tan / Rebecca Seneviratna / Samantha L Grimley / Damian F J Purcell / Stephen J Kent / Adam K Wheatley / Lin-Fa Wang / Andrew Leis / Alisa Glukhova / Marc Pellegrini / Amy W Chung / Kanta Subbarao / Adam P Uldrich / Wai-Hong Tham / Dale I Godfrey / Nicholas A Gherardin / Abstract: The development of therapeutics to prevent or treat COVID-19 remains an area of intense focus. Protein biologics, including monoclonal antibodies and nanobodies that neutralize virus, have potential ...The development of therapeutics to prevent or treat COVID-19 remains an area of intense focus. Protein biologics, including monoclonal antibodies and nanobodies that neutralize virus, have potential for the treatment of active disease. Here, we have used yeast display of a synthetic nanobody library to isolate nanobodies that bind the receptor-binding domain (RBD) of SARS-CoV-2 and neutralize the virus. We show that combining two clones with distinct binding epitopes within the RBD into a single protein construct to generate biparatopic reagents dramatically enhances their neutralizing capacity. Furthermore, the biparatopic nanobodies exhibit enhanced control over clinically relevant RBD variants that escaped recognition by the individual nanobodies. Structural analysis of biparatopic binding to spike (S) protein revealed a unique binding mode whereby the two nanobody paratopes bridge RBDs encoded by distinct S trimers. Accordingly, biparatopic nanobodies offer a way to rapidly generate powerful viral neutralizers with enhanced ability to control viral escape mutants. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28190.map.gz | 453.1 MB | EMDB map data format | |
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Header (meta data) | emd-28190-v30.xml emd-28190.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28190_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_28190.png | 40.4 KB | ||
Others | emd_28190_half_map_1.map.gz emd_28190_half_map_2.map.gz | 453.1 MB 246.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28190 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28190 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28190.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SARS-CoV-2 RBD in complex with biparatopic nanobody BP10 local refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: SARS-CoV-2 RBD in complex with biparatopic nanobody BP10...
File | emd_28190_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 RBD in complex with biparatopic nanobody BP10 local refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 RBD in complex with biparatopic nanobody BP10...
File | emd_28190_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 RBD in complex with biparatopic nanobody BP10 local refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Entire | Name: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
Supramolecule | Name: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 1 MDa |
-Supramolecule #2: SARS-CoV-2 RBD
Supramolecule | Name: SARS-CoV-2 RBD / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: BP10 biparatopic nanobody
Supramolecule | Name: BP10 biparatopic nanobody / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Macromolecule #1: SARS-CoV-2 RBD
Macromolecule | Name: SARS-CoV-2 RBD / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT ...String: NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPK |
-Macromolecule #2: BP10 biparatopic nanobody
Macromolecule | Name: BP10 biparatopic nanobody / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG LVQAGGSLRL SCAASGIIFG RNAMGWYRQA PGKERELVAA ITRNGGSTYY ADSVKGRFTI SRDNAKNTVY LQMNSLKPED TAVYYCNADP YIATYDYWGQ GTQVTVSSGG GGSGGGGSQV QLVESGGGLV QAGGSLRLSC AASGSTFWFY AMGWYRQAPG ...String: QVQLVESGGG LVQAGGSLRL SCAASGIIFG RNAMGWYRQA PGKERELVAA ITRNGGSTYY ADSVKGRFTI SRDNAKNTVY LQMNSLKPED TAVYYCNADP YIATYDYWGQ GTQVTVSSGG GGSGGGGSQV QLVESGGGLV QAGGSLRLSC AASGSTFWFY AMGWYRQAPG KERELVAAIS YSGSSTYYAD SVKGRFTISR DNAKNTVYLQ MNSLKPEDTA VYYCAKRNGV SYNYLALTNE EYDYWGQGTQ VTVSS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 / Nominal defocus max: 0.4 µm / Nominal defocus min: 2.0 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |