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Yorodumi- PDB-8aaa: Crystal structure of SARS-CoV-2 S RBD in complex with a stapled p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aaa | ||||||
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Title | Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide | ||||||
Components |
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Keywords | VIRAL PROTEIN / sRBD / Stapled peptide | ||||||
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 | Severe acute respiratory syndrome coronavirus 2 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Brear, P. / Chen, L. / Gaynor, K. / Harman, M. / Dods, R. / Hyvonen, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2. Authors: Gaynor, K.U. / Vaysburd, M. / Harman, M.A.J. / Albecka, A. / Jeffrey, P. / Beswick, P. / Papa, G. / Chen, L. / Mallery, D. / McGuinness, B. / Van Rietschoten, K. / Stanway, S. / Brear, P. / ...Authors: Gaynor, K.U. / Vaysburd, M. / Harman, M.A.J. / Albecka, A. / Jeffrey, P. / Beswick, P. / Papa, G. / Chen, L. / Mallery, D. / McGuinness, B. / Van Rietschoten, K. / Stanway, S. / Brear, P. / Lulla, A. / Ciazynska, K. / Chang, V.T. / Sharp, J. / Neary, M. / Box, H. / Herriott, J. / Kijak, E. / Tatham, L. / Bentley, E.G. / Sharma, P. / Kirby, A. / Han, X. / Stewart, J.P. / Owen, A. / Briggs, J.A.G. / Hyvonen, M. / Skynner, M.J. / James, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aaa.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aaa.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 8aaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aaa_validation.pdf.gz | 805.1 KB | Display | wwPDB validaton report |
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Full document | 8aaa_full_validation.pdf.gz | 806.3 KB | Display | |
Data in XML | 8aaa_validation.xml.gz | 11 KB | Display | |
Data in CIF | 8aaa_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/8aaa ftp://data.pdbj.org/pub/pdb/validation_reports/aa/8aaa | HTTPS FTP |
-Related structure data
Related structure data | 7z8oC 7cjfS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22074.678 Da / Num. of mol.: 1 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: Protein/peptide | Mass: 1762.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-29N / |
#4: Water | ChemComp-HOH / |
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: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 22% PEGSM, 2% Glycerol, 0.01M CoCl2, 0.2M MgCl2, 0.1M Bis TRIS PH range: 8 / Temp details: l |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 13, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.848→97.168 Å / Num. obs: 13749 / % possible obs: 91.5 % / Redundancy: 19.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.058 / Rrim(I) all: 0.254 / Net I/σ(I): 9.3 / Num. measured all: 266723 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CJF Resolution: 1.9→48.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.145
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Displacement parameters | Biso mean: 51.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.94 Å
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