[English] 日本語
![](img/lk-miru.gif)
- 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 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN / sRBD / Stapled peptide | ||||||
Function / homology | ![]() 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 / symbiont-mediated suppression of host innate immune response / 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brear, P. / Chen, L. / Gaynor, K. / Harman, M. / Dods, R. / Hyvonen, M. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7z8oC ![]() 7cjfS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 22074.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() |
---|---|
#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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||
Serial crystallography sample delivery | Method: fixed target |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.94 Å
|