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Yorodumi- PDB-7urs: Crystal Structure of SARS-CoV-2 S delta variant receptor-binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7urs | ||||||||||||
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Title | Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 2 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / SARS-CoV-2 S RBD Fab complex / SARS-CoV-2 S receptor-binding domain antibody Fab complex / COVID-19 spike protein antibody Fab complex / delta variant / 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 / 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 Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Tolbert, W.D. / Pazgier, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Front Immunol / Year: 2023 Title: The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11. Authors: Tolbert, W.D. / Chen, Y. / Sun, L. / Benlarbi, M. / Ding, S. / Manickam, R. / Pangaro, E. / Nguyen, D.N. / Gottumukkala, S. / Cote, M. / Gonzalez, F.J. / Finzi, A. / Tehrani, Z.R. / Sajadi, M.M. / Pazgier, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7urs.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7urs.ent.gz | 205.9 KB | Display | PDB format |
PDBx/mmJSON format | 7urs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7urs_validation.pdf.gz | 482.9 KB | Display | wwPDB validaton report |
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Full document | 7urs_full_validation.pdf.gz | 491.5 KB | Display | |
Data in XML | 7urs_validation.xml.gz | 24 KB | Display | |
Data in CIF | 7urs_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7urs ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7urs | HTTPS FTP |
-Related structure data
Related structure data | 7s4sSC 7urqC 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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23362.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23536.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 26167.459 Da / Num. of mol.: 1 / Mutation: L452R, T478K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 89 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.28 Å3/Da / Density % sol: 62.47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 12% PEG 8000 0.1 M sodium phosphate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2022 |
Radiation | Monochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 34224 / % possible obs: 92.3 % / Redundancy: 3 % / CC1/2: 0.97 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.081 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1302 / CC1/2: 0.803 / Rpim(I) all: 0.294 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7S4S Resolution: 2.4→41.05 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→41.05 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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