[English] 日本語
![](img/lk-miru.gif)
- PDB-7l7d: Crystal structure of SARS-CoV-2 spike RBD in complex with human m... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7l7d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895 | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / spike protein / receptor binding domain / human monoclonal antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, J. / Crowe, J.E. | ||||||
![]() | ![]() Title: Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Authors: Dong, J. / Zost, S.J. / Greaney, A.J. / Starr, T.N. / Dingens, A.S. / Chen, E.C. / Chen, R.E. / Case, J.B. / Sutton, R.E. / Gilchuk, P. / Rodriguez, J. / Armstrong, E. / Gainza, C. / Nargi, ...Authors: Dong, J. / Zost, S.J. / Greaney, A.J. / Starr, T.N. / Dingens, A.S. / Chen, E.C. / Chen, R.E. / Case, J.B. / Sutton, R.E. / Gilchuk, P. / Rodriguez, J. / Armstrong, E. / Gainza, C. / Nargi, R.S. / Binshtein, E. / Xie, X. / Zhang, X. / Shi, P.Y. / Logue, J. / Weston, S. / McGrath, M.E. / Frieman, M.B. / Brady, T. / Tuffy, K.M. / Bright, H. / Loo, Y.M. / McTamney, P.M. / Esser, M.T. / Carnahan, R.H. / Diamond, M.S. / Bloom, J.D. / Crowe Jr., J.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 267.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 474.3 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l7eC ![]() 6xc2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24100.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Antibody | Mass: 23644.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules E![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein | Mass: 24229.189 Da / Num. of mol.: 1 / Fragment: receptor binding domain (UNP residues 330-529) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
---|---|
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 225 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.19 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16% PEG3350, 0.2 M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 17, 2020 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.98 Å / Num. obs: 24896 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.5→2.63 Å / Rmerge(I) obs: 0.245 / Num. unique obs: 3598 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 6XC2 Resolution: 2.5→43.98 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.09 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -17.4857 Å / Origin y: 15.6466 Å / Origin z: 53.4486 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |