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- PDB-8dcc: SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dcc | ||||||
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Title | SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound to P2B-2F6 Fab | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Immunogen / antigen / design / vaccine / 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 | ![]() ![]() ![]() | ||||||
![]() | Dickey, T.D. / Tolia, N.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response. Authors: Dickey, T.H. / Tang, W.K. / Butler, B. / Ouahes, T. / Orr-Gonzalez, S. / Salinas, N.D. / Lambert, L.E. / Tolia, N.H. #1: Journal: Biorxiv / Year: 2021 Title: Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response. Authors: Dickey, T.H. / Tang, W.K. / Butler, B. / Ouahes, T. / Orr-Gonzalez, S. / Salinas, N.D. / Lambert, L.E. / Tolia, N.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.7 KB | Display | ![]() |
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PDB format | ![]() | 104.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.8 KB | Display | ![]() |
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Full document | ![]() | 469.5 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dceC ![]() 7bwjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23684.422 Da / Num. of mol.: 1 / Fragment: RBD SPEEDesign Immunogen 3 (UNP residues 333-526) Mutation: T333K, A363Y, N388K, N394Y, I468T, S514T, H519D, A522P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Wuhan-Hu-1 / Gene: S, 2 / Plasmid: pHLsec / Cell line (production host): Expi293F / Production host: ![]() |
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#2: Antibody | Mass: 22686.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 25600.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M sodium fluoride, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→70.88 Å / Num. obs: 23841 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.078 / Rrim(I) all: 0.203 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.57→2.66 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.089 / Num. unique obs: 2326 / CC1/2: 0.332 / Rpim(I) all: 0.861 / Rrim(I) all: 2.262 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7BWJ Resolution: 2.6→56.23 Å / SU ML: 0.4207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4868 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→56.23 Å
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Refine LS restraints |
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LS refinement shell |
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