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- PDB-7vng: Crystal structure of human coronavirus 229E spike protein recepto... -
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Open data
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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 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / human coronavirus 229E / spike protein / RBD / antibody / S11 / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiang, J.C. / Zhao, W.W. / Yang, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.3 KB | Display | ![]() |
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PDB format | ![]() | 176.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.9 KB | Display | ![]() |
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Full document | ![]() | 486.7 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vmzC ![]() 7vn9SC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() | ||
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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.) ![]() Production host: ![]() ![]() | ||
#3: Antibody | Mass: 23345.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||
#4: Sugar | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |