+Open data
-Basic information
Entry | Database: PDB / ID: 7xsw | ||||||
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Title | Structure of SARS-CoV-2 antibody S309 with GX/P2V/2017 RBD | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / GX/P2V/2017 / RBD / antibody / S309 / Fab / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Pangolin coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Jia, Y.F. / Chai, Y. / Wang, Q.H. / Gao, G.F. | ||||||
Funding support | 1items
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Citation | Journal: Cell Rep / Year: 2022 Title: Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017. Authors: Jia, Y. / Niu, S. / Hu, Y. / Chai, Y. / Zheng, A. / Su, C. / Wu, L. / Han, P. / Han, P. / Lu, D. / Liu, Z. / Yan, X. / Tian, D. / Chen, Z. / Qi, J. / Tian, W.X. / Wang, Q. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xsw.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xsw.ent.gz | 198.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/7xsw ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xsw | HTTPS FTP |
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-Related structure data
Related structure data | 7xnfC 7r6xS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25386.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23291.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 24237.365 Da / Num. of mol.: 2 / Fragment: BetaCoV S1-CTD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pangolin coronavirus / Production host: Homo sapiens (human) / References: UniProt: A0A6G6A2Q2 #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...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 Has ligand of interest | Y | |
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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: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M magnesium chloride hexahydrate, 0.1M MES (pH 6.0), 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 40975 / % possible obs: 89 % / Redundancy: 4.94 % / Rrim(I) all: 3.421 / Net I/σ(I): 1.9 |
Reflection shell | Resolution: 3.3→3.5 Å / Num. unique obs: 6611 / Rrim(I) all: 3.303 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7R6X Resolution: 3.3→48.54 Å / SU ML: 0.663 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.6184 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: 75.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→48.54 Å
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Refine LS restraints |
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LS refinement shell |
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