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Yorodumi- PDB-7np1: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7np1 | ||||||
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Title | Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Antibody Immune System | ||||||
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: 2.8 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 | 7np1.cif.gz | 581.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7np1.ent.gz | 385.7 KB | Display | PDB format |
PDBx/mmJSON format | 7np1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7np1_validation.pdf.gz | 958.4 KB | Display | wwPDB validaton report |
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Full document | 7np1_full_validation.pdf.gz | 994.1 KB | Display | |
Data in XML | 7np1_validation.xml.gz | 81.4 KB | Display | |
Data in CIF | 7np1_validation.cif.gz | 110.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/7np1 ftp://data.pdbj.org/pub/pdb/validation_reports/np/7np1 | HTTPS FTP |
-Related structure data
Related structure data | 7bnvSC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Antibody , 2 types, 8 molecules HIJKLMNO
#2: Antibody | Mass: 23397.207 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23759.311 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Protein / Non-polymers , 2 types, 75 molecules ABCD
#1: Protein | Mass: 26099.357 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 4 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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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: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16% PEG3350 0.2 M ammonium 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: 0.965459 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.33 Å / Num. obs: 85521 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 66.65 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.0629 / Net I/σ(I): 5.79 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 8446 / CC1/2: 0.494 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BNV Resolution: 2.8→48.28 Å / SU ML: 0.4344 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.2544 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: 64.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.28 Å
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Refine LS restraints |
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LS refinement shell |
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