+Open data
-Basic information
Entry | Database: PDB / ID: 7c02 | ||||||
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Title | Crystal structure of dimeric MERS-CoV receptor binding domain | ||||||
Components | Spike glycoproteinSpike protein | ||||||
Keywords | VIRAL PROTEIN / MERS-CoV / Receptor Binding Domain / Vaccine / VIRUS | ||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / 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 / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Dai, L. / Qi, J. / Gao, G.F. | ||||||
Citation | Journal: Cell / Year: 2020 Title: A Universal Design of Betacoronavirus Vaccines against COVID-19, MERS, and SARS. Authors: Dai, L. / Zheng, T. / Xu, K. / Han, Y. / Xu, L. / Huang, E. / An, Y. / Cheng, Y. / Li, S. / Liu, M. / Yang, M. / Li, Y. / Cheng, H. / Yuan, Y. / Zhang, W. / Ke, C. / Wong, G. / Qi, J. / Qin, ...Authors: Dai, L. / Zheng, T. / Xu, K. / Han, Y. / Xu, L. / Huang, E. / An, Y. / Cheng, Y. / Li, S. / Liu, M. / Yang, M. / Li, Y. / Cheng, H. / Yuan, Y. / Zhang, W. / Ke, C. / Wong, G. / Qi, J. / Qin, C. / Yan, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c02.cif.gz | 195 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c02.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 7c02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/7c02 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/7c02 | HTTPS FTP |
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-Related structure data
Related structure data | 4kqzS 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
#1: Protein | Mass: 27114.447 Da / Num. of mol.: 2 / Fragment: Receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A0A0Q7F3, UniProt: K9N5Q8*PLUS #2: Sugar | ChemComp-NAG / | 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: 2.92 Å3/Da / Density % sol: 57.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.12M Ehylene Glycols, 0.1M Imidazole MES, 30% v/v Glycerol, PEG 4000 |
-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: Jan 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 14565 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 52.22 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.9→3 Å / Num. unique obs: 1406 / CC1/2: 0.699 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KQZ Resolution: 2.91→37.34 Å / SU ML: 0.2754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8706 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: 52.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.91→37.34 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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