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Yorodumi- PDB-7vng: Crystal structure of human coronavirus 229E spike protein recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vng | ||||||
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Title | Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with S11 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / human coronavirus 229E / spike protein / RBD / antibody / S11 / IMMUNE SYSTEM / 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 / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human coronavirus 229E Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Xiang, J.C. / Zhao, W.W. / Yang, B. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Antigenic mapping reveals sites of vulnerability on alpha-HCoV spike protein. Authors: Xiang, J. / Su, J. / Lan, Q. / Zhao, W. / Zhou, Y. / Xu, Y. / Niu, J. / Xia, S. / Qi, Q. / Sidhu, S. / Lu, L. / Miersch, S. / Yang, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vng.cif.gz | 259.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vng.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/7vng ftp://data.pdbj.org/pub/pdb/validation_reports/vn/7vng | HTTPS FTP |
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-Related structure data
Related structure data | 7vmzC 7vn9SC 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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Unit cell |
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-Components
#1: Protein | Mass: 16194.324 Da / Num. of mol.: 1 / Fragment: receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15423 | ||
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#2: Antibody | Mass: 23277.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | ||
#3: Antibody | Mass: 23345.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | ||
#4: Sugar | 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: 3.85 Å3/Da / Density % sol: 68.02 % / Description: block |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.6M Sodium Formate, 10% Glycerol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→68.1 Å / Num. obs: 20687 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 154.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.059 / Rrim(I) all: 0.212 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.65→4 Å / Redundancy: 13.1 % / Rmerge(I) obs: 3.116 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2600 / CC1/2: 0.546 / Rpim(I) all: 1.229 / Rrim(I) all: 3.242 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VN9 Resolution: 3.8→49.07 Å / SU ML: 0.6579 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5043 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: 182.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→49.07 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: 2.63474504498 Å / Origin y: 60.272840023 Å / Origin z: 23.4260412009 Å
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Refinement TLS group | Selection details: all |