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Yorodumi- PDB-7kgk: Crystal structure of synthetic nanobody (Sb16) complexes with SAR... -
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-Basic information
Entry | Database: PDB / ID: 7kgk | ||||||
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Title | Crystal structure of synthetic nanobody (Sb16) complexes with SARS-CoV-2 receptor binding domain | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / Spike Protein / RBD / Antibody / Nanobody / Sybody / Epitope / Neutralization | ||||||
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 / membrane fusion / Attachment and Entry / 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 | Severe acute respiratory syndrome coronavirus 2 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Jiang, J. / Ahmad, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H. | ||||||
Citation | Journal: J Biol Chem / Year: 2021 Title: Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. Authors: Javeed Ahmad / Jiansheng Jiang / Lisa F Boyd / Allison Zeher / Rick Huang / Di Xia / Kannan Natarajan / David H Margulies / Abstract: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of ...Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures. #1: Journal: Biorxiv / Year: 2021 Title: Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes. Authors: Ahmad, J. / Jiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kgk.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kgk.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kgk_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 7kgk_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 7kgk_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7kgk_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/7kgk ftp://data.pdbj.org/pub/pdb/validation_reports/kg/7kgk | HTTPS FTP |
-Related structure data
Related structure data | 7kgjC 7klwC 7mfuC 7mfvC 7n0gC 7n0hC 7bz5S C: citing same article (ref.) S: Starting model for refinement |
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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: Protein | Mass: 21873.496 Da / Num. of mol.: 1 / Fragment: receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2 |
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#2: Antibody | Mass: 13158.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli MC1061 (bacteria) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% PEG 20000, and 0.1M Hepes pH 7.0 / PH range: 5.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→57.34 Å / Num. obs: 13219 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 39.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1185 / CC1/2: 0.987 / Rpim(I) all: 0.134 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BZ5 Resolution: 2.6→56.09 Å / SU ML: 0.3994 / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Phase error: 33.7121 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: 59.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→56.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.883635080906 Å / Origin y: 20.105518747 Å / Origin z: 12.3410938873 Å
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Refinement TLS group | Selection details: all |