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Yorodumi- PDB-7cjf: Crystal structure of SARS-CoV-2 RBD in complex with a neutralizin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cjf | |||||||||
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Title | Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody Fab | |||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / RBD / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 Å | |||||||||
Authors | Guo, Y. / Li, X. / Zhang, G. / Fu, D. / Schweizer, L. / Zhang, H. / Rao, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: A SARS-CoV-2 neutralizing antibody with extensive Spike binding coverage and modified for optimal therapeutic outcomes. Authors: Guo, Y. / Huang, L. / Zhang, G. / Yao, Y. / Zhou, H. / Shen, S. / Shen, B. / Li, B. / Li, X. / Zhang, Q. / Chen, M. / Chen, D. / Wu, J. / Fu, D. / Zeng, X. / Feng, M. / Pi, C. / Wang, Y. / ...Authors: Guo, Y. / Huang, L. / Zhang, G. / Yao, Y. / Zhou, H. / Shen, S. / Shen, B. / Li, B. / Li, X. / Zhang, Q. / Chen, M. / Chen, D. / Wu, J. / Fu, D. / Zeng, X. / Feng, M. / Pi, C. / Wang, Y. / Zhou, X. / Lu, M. / Li, Y. / Fang, Y. / Lu, Y.Y. / Hu, X. / Wang, S. / Zhang, W. / Gao, G. / Adrian, F. / Wang, Q. / Yu, F. / Peng, Y. / Gabibov, A.G. / Min, J. / Wang, Y. / Huang, H. / Stepanov, A. / Zhang, W. / Cai, Y. / Liu, J. / Yuan, Z. / Zhang, C. / Lou, Z. / Deng, F. / Zhang, H. / Shan, C. / Schweizer, L. / Sun, K. / Rao, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cjf.cif.gz | 282.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cjf.ent.gz | 224.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/7cjf ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cjf | HTTPS FTP |
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-Related structure data
Related structure data | 7bwjS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 24271.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23281.793 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: Protein | Mass: 21772.391 Da / Num. of mol.: 1 / Fragment: receptor binding domain, RBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2 |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.94 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: 20%(w/v)PEG 3350 0.2M potassium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 49623 / % possible obs: 92.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.031 / Rrim(I) all: 0.097 / Χ2: 0.958 / Net I/σ(I): 7.9 / Num. measured all: 475973 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BWJ Resolution: 2.108→36.164 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.04 / 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 max: 163.34 Å2 / Biso mean: 39.1355 Å2 / Biso min: 16.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.108→36.164 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 1.5016 Å / Origin y: -32.9337 Å / Origin z: -5.522 Å
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Refinement TLS group |
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