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Yorodumi- PDB-7can: Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7can | |||||||||
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Title | Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Receptor-binding domain (RBD) | |||||||||
Components |
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Keywords | PROTEIN BINDING / coronavirus / Covid-19 / nanobody / neutralizing antibody / receptor binding protein / SARS-CoV-2 / S protein / synthetic antibody / VHH. | |||||||||
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | synthetic construct (others) Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | |||||||||
Authors | Li, T. / Yao, H. / Cai, H. / Qin, W. / Li, D. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Authors: Tingting Li / Hongmin Cai / Hebang Yao / Bingjie Zhou / Ning Zhang / Martje Fentener van Vlissingen / Thijs Kuiken / Wenyu Han / Corine H GeurtsvanKessel / Yuhuan Gong / Yapei Zhao / Quan ...Authors: Tingting Li / Hongmin Cai / Hebang Yao / Bingjie Zhou / Ning Zhang / Martje Fentener van Vlissingen / Thijs Kuiken / Wenyu Han / Corine H GeurtsvanKessel / Yuhuan Gong / Yapei Zhao / Quan Shen / Wenming Qin / Xiao-Xu Tian / Chao Peng / Yanling Lai / Yanxing Wang / Cedric A J Hutter / Shu-Ming Kuo / Juan Bao / Caixuan Liu / Yifan Wang / Audrey S Richard / Hervé Raoul / Jiaming Lan / Markus A Seeger / Yao Cong / Barry Rockx / Gary Wong / Yuhai Bi / Dimitri Lavillette / Dianfan Li / Abstract: SARS-CoV-2, the causative agent of COVID-19, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein. Neutralizing antibodies that block RBD-ACE2 interaction are candidates ...SARS-CoV-2, the causative agent of COVID-19, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (K = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC = 0.42 μg mL). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7can.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7can.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 7can.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7can_validation.pdf.gz | 799.4 KB | Display | wwPDB validaton report |
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Full document | 7can_full_validation.pdf.gz | 802.1 KB | Display | |
Data in XML | 7can_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7can_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/7can ftp://data.pdbj.org/pub/pdb/validation_reports/ca/7can | HTTPS FTP |
-Related structure data
Related structure data | 7c8vC 7c8wC 5m13S 6m0jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 16573.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Protein | Mass: 23747.643 Da / Num. of mol.: 1 / Fragment: Receptor-binding domain (RBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): High5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2 |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Chemical | ChemComp-GOL / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 66.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→49.9 Å / Num. obs: 11305 / % possible obs: 99.9 % / Redundancy: 18.4 % / Biso Wilson estimate: 85.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.072 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.714 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1780 / CC1/2: 0.735 / Rpim(I) all: 0.385 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M0J, 5M13 Resolution: 2.94→49.9 Å / SU ML: 0.4184 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2687 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.38 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→49.9 Å
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Refine LS restraints |
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LS refinement shell |
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