+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28189 | |||||||||
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Title | SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 | |||||||||
Map data | SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 | |||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.19 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_28189.map.gz | 461.7 MB | EMDB map data format | |
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Header (meta data) | emd-28189-v30.xml emd-28189.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28189_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_28189.png | 35.4 KB | ||
Others | emd_28189_half_map_1.map.gz emd_28189_half_map_2.map.gz | 452.9 MB 452.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28189 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28189 | HTTPS FTP |
-Validation report
Summary document | emd_28189_validation.pdf.gz | 888.3 KB | Display | EMDB validaton report |
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Full document | emd_28189_full_validation.pdf.gz | 887.9 KB | Display | |
Data in XML | emd_28189_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | emd_28189_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28189 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28189 | HTTPS FTP |
-Related 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_28189.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 Spike in complex with biparatopic nanobody BP10 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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 Spike in complex with biparatopic nanobody BP10
File | emd_28189_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 Spike in complex with biparatopic nanobody BP10
File | emd_28189_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 Spike in complex with biparatopic nanobody BP10 | ||||||||||||
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 Spike
Supramolecule | Name: SARS-CoV-2 Spike / 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 Spike
Macromolecule | Name: SARS-CoV-2 Spike / 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: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PASVGSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQ |
-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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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.4 µm / Nominal defocus min: 2.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |