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Yorodumi- PDB-8sir: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -
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-Basic information
Entry | Database: PDB / ID: 8sir | ||||||
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Title | Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC25.54 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / bnAb / SARS-CoV-2 / broadly neutralizing antibody / spike / RBD | ||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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: 3.3 Å | ||||||
Authors | Liu, H. / Wilson, I.A. | ||||||
Funding support | United States, 1items
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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. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. ...Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A. / Li, X. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A. / Burton, D. / Wilson, I. / Andrabi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sir.cif.gz | 258.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sir.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 8sir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sir_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 8sir_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 8sir_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 8sir_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/8sir ftp://data.pdbj.org/pub/pdb/validation_reports/si/8sir | HTTPS FTP |
-Related structure data
Related structure data | 8siqC 8sisC 8sitC 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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Unit cell |
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-Components
#1: Protein | Mass: 23104.867 Da / Num. of mol.: 1 / 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 |
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#2: Antibody | Mass: 25803.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) |
#3: Antibody | Mass: 23574.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) |
#4: Sugar | ChemComp-NAG / |
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: 3.2 Å3/Da / Density % sol: 61.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2 M potassium sodium tartrate, pH 7.2 |
-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: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→50 Å / Num. obs: 14256 / % possible obs: 99.8 % / Redundancy: 11.5 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.091 / Rrim(I) all: 0.312 / Χ2: 0.913 / Net I/σ(I): 2.8 / Num. measured all: 164569 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.76 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.44 / 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 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→48.76 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -47.16 Å / Origin y: 50.0553 Å / Origin z: 10.0501 Å
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Refinement TLS group | Selection details: all |