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Yorodumi- PDB-8h91: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -
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-Basic information
Entry | Database: PDB / ID: 8h91 | ||||||
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Title | Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Spike receptor-binding domain nanobody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / 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 Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å | ||||||
Authors | Zhang, Y.T. / Li, J. / Zhang, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19 Authors: Zhang, Y.T. / Li, J. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h91.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h91.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 8h91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h91_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 8h91_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 8h91_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 8h91_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/8h91 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/8h91 | HTTPS FTP |
-Related structure data
Related structure data | 7w1sS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21772.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2 #2: Antibody | Mass: 12568.915 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1%(w/v) Tryptone, 0.001 M Sodiumazide, 0.05 M HepesSodium pH7.0, 20%(w/v) polyethyleneglycol3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 3.07→55.55 Å / Num. obs: 14976 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 56.998 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.07→3.23 Å / Rmerge(I) obs: 1.413 / Num. unique obs: 2124 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W1S Resolution: 3.07→55.54 Å / SU ML: 0.463565732501 / Cross valid method: THROUGHOUT / σ(F): 1.338 / Phase error: 27.5093856822 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: 43.5462081597 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.07→55.54 Å
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Refine LS restraints |
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LS refinement shell |
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