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Yorodumi- PDB-7bnv: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bnv | ||||||
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Title | Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-300 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Antibody Immune System | ||||||
Function / homology | Function and homology information : / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Hall, G. / Cowan, R. / Carr, M. | ||||||
Citation | Journal: Front Immunol / Year: 2021 Title: Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses. Authors: Bullen, G. / Galson, J.D. / Hall, G. / Villar, P. / Moreels, L. / Ledsgaard, L. / Mattiuzzo, G. / Bentley, E.M. / Masters, E.W. / Tang, D. / Millett, S. / Tongue, D. / Brown, R. / ...Authors: Bullen, G. / Galson, J.D. / Hall, G. / Villar, P. / Moreels, L. / Ledsgaard, L. / Mattiuzzo, G. / Bentley, E.M. / Masters, E.W. / Tang, D. / Millett, S. / Tongue, D. / Brown, R. / Diamantopoulos, I. / Parthiban, K. / Tebbutt, C. / Leah, R. / Chaitanya, K. / Ergueta-Carballo, S. / Pazeraitis, D. / Surade, S.B. / Ashiru, O. / Crippa, L. / Cowan, R. / Bowler, M.W. / Campbell, J.I. / Lee, W.J. / Carr, M.D. / Matthews, D. / Pfeffer, P. / Hufton, S.E. / Sawmynaden, K. / Osbourn, J. / McCafferty, J. / Karatt-Vellatt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bnv.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bnv.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bnv_validation.pdf.gz | 459.5 KB | Display | wwPDB validaton report |
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Full document | 7bnv_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 7bnv_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 7bnv_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/7bnv ftp://data.pdbj.org/pub/pdb/validation_reports/bn/7bnv | HTTPS FTP |
-Related structure data
Related structure data | 7np1C 6m0jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26308.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Homo sapiens (human) / References: UniProt: A0A6M5UN06 |
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#2: Protein | Mass: 24528.439 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: Antibody | Mass: 23892.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350 0.3 M potassium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40.23 Å / Num. obs: 32467 / % possible obs: 99.08 % / Redundancy: 1.9 % / Biso Wilson estimate: 56.48 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.34 |
Reflection shell | Resolution: 2.35→2.434 Å / Num. unique obs: 3234 / CC1/2: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M0J Resolution: 2.35→40.23 Å / SU ML: 0.3534 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.5911 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: 70 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→40.23 Å
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Refine LS restraints |
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LS refinement shell |
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