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Yorodumi- PDB-8sdg: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sdg | ||||||||||||
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Title | Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.43 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / SARS-CoV-2 / coronavirus / antibody | ||||||||||||
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 / 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||||||||
Authors | Yuan, M. / Wilson, I.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biorxiv / Year: 2023 Title: Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift. Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R.N. / Torres, J.L. / He, W.T. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / ...Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R.N. / Torres, J.L. / He, W.T. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A.L. / Li, X. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A.B. / Burton, D.R. / Wilson, I.A. / Andrabi, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sdg.cif.gz | 249 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sdg.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 8sdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sdg_validation.pdf.gz | 496.2 KB | Display | wwPDB validaton report |
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Full document | 8sdg_full_validation.pdf.gz | 525.9 KB | Display | |
Data in XML | 8sdg_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 8sdg_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/8sdg ftp://data.pdbj.org/pub/pdb/validation_reports/sd/8sdg | HTTPS FTP |
-Related structure data
Related structure data | 8sdfC 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: 24064.057 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: 23533.100 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: 23104.867 Da / Num. of mol.: 2 / Fragment: Receptor binding domain, UNP residues 333-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2 #4: Sugar | ChemComp-NAG / | 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: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1.0 M Li-chloride, 10% PEG-6000, and 0.1 M citric acid pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→153.213 Å / Num. obs: 47774 / % possible obs: 93.4 % / Redundancy: 5.2 % / CC1/2: 0.995 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.71→2.76 Å / Num. unique obs: 2451 / CC1/2: 0.495 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→72.84 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.39 / 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: 2.71→72.84 Å
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Refine LS restraints |
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LS refinement shell |
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