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Yorodumi- EMDB-12465: SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12465 | |||||||||
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Title | SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nanobody / Spike / Complex / Dimer / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Das H / Hallberg BM | |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Authors: Leo Hanke / Hrishikesh Das / Daniel J Sheward / Laura Perez Vidakovics / Egon Urgard / Ainhoa Moliner-Morro / Changil Kim / Vivien Karl / Alec Pankow / Natalie L Smith / Bartlomiej Porebski ...Authors: Leo Hanke / Hrishikesh Das / Daniel J Sheward / Laura Perez Vidakovics / Egon Urgard / Ainhoa Moliner-Morro / Changil Kim / Vivien Karl / Alec Pankow / Natalie L Smith / Bartlomiej Porebski / Oscar Fernandez-Capetillo / Erdinc Sezgin / Gabriel K Pedersen / Jonathan M Coquet / B Martin Hällberg / Ben Murrell / Gerald M McInerney / Abstract: Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the ...Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants. | |||||||||
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_12465.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-12465-v30.xml emd-12465.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_12465.png | 68.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12465 | HTTPS FTP |
-Related structure data
Related structure data | 7nllMC 7ns6C 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_12465.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.01 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 : Spike RBD (two molecules) in complex with two FU2 nanobodies
Entire | Name: Spike RBD (two molecules) in complex with two FU2 nanobodies |
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Components |
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-Supramolecule #1: Spike RBD (two molecules) in complex with two FU2 nanobodies
Supramolecule | Name: Spike RBD (two molecules) in complex with two FU2 nanobodies type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 35.7 KDa |
-Supramolecule #2: Receptor Binding Domain of SARS-CoV-2 spike glycoprotein
Supramolecule | Name: Receptor Binding Domain of SARS-CoV-2 spike glycoprotein type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Nanobody Fu2
Supramolecule | Name: Nanobody Fu2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Macromolecule #1: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 25.643859 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF ...String: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNGGLPET GG UniProtKB: Spike glycoprotein |
-Macromolecule #2: Nanobody Fu2
Macromolecule | Name: Nanobody Fu2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 15.859231 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG LVQPGGSLRL SCAASGFTLD DYAIGWFRQA PGKEREGVSF ITSSDGSTYY VDSVKGRFTI SRDNAKNTVY LQMNSLTPE DTAIYYCAVG PSFSYTGSTY YRSELPWDYD YWGQGTQVTV SSGGLPETGG HHHHHH |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / 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
Concentration | 2.1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 14081 / Average exposure time: 1.5 sec. / Average electron dose: 48.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final 3D classification | Software - Name: cryoSPARC (ver. 3.0.1) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.0.1) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.1) / Number images used: 277372 |