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Yorodumi- PDB-7xsa: Crystal structure of SARS-CoV-2 spike receptor binding domain bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xsa | ||||||
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Title | Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P2S-2E9 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 spike / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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: 2.2 Å | ||||||
Authors | Wang, X. / Wang, Z. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Immunol. / Year: 2023 Title: Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants. Authors: Ju, B. / Zhang, Q. / Wang, Z. / Aw, Z.Q. / Chen, P. / Zhou, B. / Wang, R. / Ge, X. / Lv, Q. / Cheng, L. / Zhang, R. / Wong, Y.H. / Chen, H. / Wang, H. / Shan, S. / Liao, X. / Shi, X. / Liu, ...Authors: Ju, B. / Zhang, Q. / Wang, Z. / Aw, Z.Q. / Chen, P. / Zhou, B. / Wang, R. / Ge, X. / Lv, Q. / Cheng, L. / Zhang, R. / Wong, Y.H. / Chen, H. / Wang, H. / Shan, S. / Liao, X. / Shi, X. / Liu, L. / Chu, J.J.H. / Wang, X. / Zhang, Z. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xsa.cif.gz | 242.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xsa.ent.gz | 191.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xsa_validation.pdf.gz | 485.5 KB | Display | wwPDB validaton report |
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Full document | 7xsa_full_validation.pdf.gz | 501.9 KB | Display | |
Data in XML | 7xsa_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 7xsa_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/7xsa ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xsa | HTTPS FTP |
-Related structure data
Related structure data | 7xs8C 7xsbC 7xscC 6m0jS 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: 23451.561 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: 22608.914 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: 27105.496 Da / Num. of mol.: 2 / Fragment: receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2 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: 2.49 Å3/Da / Density % sol: 55.29 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 15% v/v 2-Propanol, 0.1M Sodium citrate tribasic dihydrate pH 4.8, 11% w/v Polyethylene glycol 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 23, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 72654 / % possible obs: 99.1 % / Redundancy: 5.6 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.045 / Rrim(I) all: 0.108 / Χ2: 0.999 / Net I/σ(I): 5.5 / Num. measured all: 408404 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M0J Resolution: 2.2→32.41 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.16 / 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: 2.2→32.41 Å
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Refine LS restraints |
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LS refinement shell |
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