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Yorodumi- PDB-6jhy: Crystal Structure of the S1 subunit N-terminal domain from DcCoV ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jhy | |||||||||||||||
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Title | Crystal Structure of the S1 subunit N-terminal domain from DcCoV UAE-HKU23 spike protein | |||||||||||||||
Components | Spike protein | |||||||||||||||
Keywords | VIRAL PROTEIN / DcCoV UAE-HKU23 / Spike (S) / N-terminal domain (NTD) / Crystal Structure | |||||||||||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / membrane => GO:0016020 / 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 / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||||||||
Biological species | Dromedary camel coronavirus HKU23 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||||||||
Authors | Lu, G. / Cheng, Y. / Ye, F. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Virology / Year: 2019 Title: Crystal structure of the S1 subunit N-terminal domain from DcCoV UAE-HKU23 spike protein. Authors: Cheng, Y. / He, B. / Yang, J. / Ye, F. / Lin, S. / Yang, F. / Chen, Z. / Chen, Z. / Cao, Y. / Lu, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jhy.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jhy.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 6jhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jhy_validation.pdf.gz | 1007.7 KB | Display | wwPDB validaton report |
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Full document | 6jhy_full_validation.pdf.gz | 1008.8 KB | Display | |
Data in XML | 6jhy_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6jhy_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/6jhy ftp://data.pdbj.org/pub/pdb/validation_reports/jh/6jhy | HTTPS FTP |
-Related structure data
Related structure data | 4h14S 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: 32843.223 Da / Num. of mol.: 1 / Fragment: NTD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dromedary camel coronavirus HKU23 / Gene: AHN64783.1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: X2JHN8 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.5 M Ammonium sulfate, and 0.1 M Sodium acetate trihydrate, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32.61 Å / Num. obs: 14536 / % possible obs: 99.49 % / Redundancy: 4.9 % / Rpim(I) all: 0.058 / Rsym value: 0.118 / Net I/σ(I): 14.826 |
Reflection shell | Resolution: 2.5→2.59 Å / Rpim(I) all: 0.147 / Rsym value: 0.299 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H14 Resolution: 2.5→32.61 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→32.61 Å
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Refine LS restraints |
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LS refinement shell |
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