[English] 日本語
Yorodumi- PDB-2ieq: Core Structure of S2 from the Human Coronavirus NL63 Spike Glycop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ieq | ||||||
---|---|---|---|---|---|---|---|
Title | Core Structure of S2 from the Human Coronavirus NL63 Spike Glycoprotein | ||||||
Components | Spike glycoproteinSpike protein | ||||||
Keywords | VIRAL PROTEIN / Human coronavirus / membrane fusion / S2 / virus entry / six-helix bundle | ||||||
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 / host cell surface receptor binding / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å | ||||||
Authors | Liu, J. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Core Structure of S2 from the Human Coronavirus NL63 Spike Glycoprotein Authors: Zheng, Q. / Deng, Y. / Liu, J. / Hoek, L.V. / Berkhout, B. / Lu, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ieq.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ieq.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ieq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2ieq ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2ieq | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zv8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a trimer of dimers, i.e. six-helix bundle |
-Components
#1: Protein | Mass: 11722.983 Da / Num. of mol.: 3 Fragment: residues 981-1038, 1242-1283 connected by 10-mer link Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus / Genus: Coronavirus / Strain: NL63Human coronavirus NL63 / Gene: S / Plasmid: pAE4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6Q1S2 #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.1 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 400, sodium acetate, Imidazole, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 4, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.747→51.57 Å / Num. all: 25668 / Num. obs: 25668 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.747→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2573 / % possible all: 98.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZV8 Resolution: 1.747→51.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.557 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.486 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.747→51.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.747→1.792 Å / Total num. of bins used: 20
|