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Yorodumi- PDB-7ps5: Crystal structure of the receptor binding domain of SARS-CoV-2 be... -
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Basic information
| Entry | Database: PDB / ID: 7ps5 | |||||||||
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| Title | Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-47 Fab | |||||||||
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Keywords | VIRAL PROTEIN / SARS-COV-2 B.1.1.7 (Alpha) VARIANT / B.1.351 (Beta) VARIANT / P.1 (Gamma) VARIANT / B.1.617.2 (Delta) VARIANT / ANTIBODY / RECEPTOR-BINDING-DOMAIN / SPIKE / NEUTRALISATION / VIRAL PROTEIN/IMMUNE SYSTEM / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | |||||||||
| Function / homology | Function and homology informationsymbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 | Homo sapiens (human)![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å | |||||||||
Authors | Zhou, D. / Ren, J. / Stuart, D.I. | |||||||||
| Funding support | United Kingdom, 2items
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Citation | Journal: Cell Host Microbe / Year: 2022Title: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James ...Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James Brett Case / Yuguang Zhao / Donal T Skelly / Rita E Chen / Sile Ann Johnson / Thomas G Ritter / Chris Mason / Tariq Malik / Nigel Temperton / Neil G Paterson / Mark A Williams / David R Hall / Daniel K Clare / Andrew Howe / Philip J R Goulder / Elizabeth E Fry / Michael S Diamond / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton / ![]() Abstract: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape ...Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7ps5.cif.gz | 322.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7ps5.ent.gz | 220.1 KB | Display | PDB format |
| PDBx/mmJSON format | 7ps5.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7ps5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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| Full document | 7ps5_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | 7ps5_validation.xml.gz | 23.7 KB | Display | |
| Data in CIF | 7ps5_validation.cif.gz | 31.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/7ps5 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/7ps5 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7pryC ![]() 7przC ![]() 7ps0C ![]() 7ps1C ![]() 7ps2C ![]() 7ps3C ![]() 7ps4C ![]() 7ps6C ![]() 7ps7C ![]() 7q0gC ![]() 7q0hC ![]() 7q0iC ![]() 7q6eC ![]() 7q9fC ![]() 7q9gC ![]() 7q9iC ![]() 7q9jC ![]() 7q9kC ![]() 7q9mC ![]() 7q9pC ![]() 7orbS C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
| #1: Antibody | Mass: 24438.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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| #2: Antibody | Mass: 23591.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
| #3: Protein | Mass: 23646.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
| #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
| #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
| Has ligand of interest | N |
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 5.44 Å3/Da / Density % sol: 77.39 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Potassium chloride, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 2000 MME |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å |
| Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2021 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 |
| Reflection | Resolution: 3.14→60 Å / Num. obs: 27125 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 115.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.068 / Net I/σ(I): 7.8 |
| Reflection shell | Resolution: 3.14→3.2 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1313 / CC1/2: 0.365 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 7ORB Resolution: 3.14→57.35 Å / SU ML: 0.7635 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8284 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 129.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.14→57.35 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 | Refine-ID: X-RAY DIFFRACTION
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United Kingdom, 2items
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