[English] 日本語
Yorodumi- PDB-4c7w: Crystal structure of Mouse Hepatitis virus strain S Hemagglutinin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c7w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Mouse Hepatitis virus strain S Hemagglutinin- esterase in complex with 4-O-acetylated sialic acid | |||||||||
Components | HEMAGGLUTININ-ESTERASEHemagglutinin esterase | |||||||||
Keywords | HYDROLASE / RECEPTOR DESTROYING / RECEPTOR BINDING | |||||||||
Function / homology | Function and homology information sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | MURINE HEPATITIS VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Zeng, Q.H. / Huizinga, E.G. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: The Murine Coronavirus Hemagglutinin-Esterase Receptor-Binding Site: A Major Shift in Ligand Specificity Through Modest Changes in Architecture. Authors: Langereis, M.A. / Zeng, Q. / Heesters, B.A. / Huizinga, E.G. / De Groot, R.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c7w.cif.gz | 303 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c7w.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/4c7w ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c7w | HTTPS FTP |
---|
-Related structure data
Related structure data | 4c7lSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43503.355 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-403 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MURINE HEPATITIS VIRUS / Strain: S / Plasmid: PCD5- MHV-S-HE-T-FC / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) References: UniProt: O55252, UniProt: P31614*PLUS, sialate O-acetylesterase |
---|
-Sugars , 5 types, 14 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | #7: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 3 types, 78 molecules
#6: Chemical | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
---|---|
Crystal grow | pH: 3.6 Details: 0.2 M KH2PO4, 0.2 M SODIUM MALONATE, 15% (W/V) PEG3350 AND 5% (W/V) GLYCEROL, pH 3.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 11, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→54.5 Å / Num. obs: 46670 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C7L Resolution: 2.5→83.92 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.042 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 45.024 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→83.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|