[English] 日本語
Yorodumi- PDB-5e30: Crystal structure of H5 hemagglutinin Q226L mutant from the influ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+30 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/duck/Egypt/10185SS/2010 (H5N1) with LSTc | |||||||||
Components | (Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / H5N1 influenza virus / hemagglutinin / receptor binding specificity / transmission / glycan complex | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Zhu, X. / Wilson, I.A. | |||||||||
Citation | Journal: Cell Rep / Year: 2015 Title: Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants. Authors: Zhu, X. / Viswanathan, K. / Raman, R. / Yu, W. / Sasisekharan, R. / Wilson, I.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5e30.cif.gz | 317.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5e30.ent.gz | 256.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/5e30 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/5e30 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5e2ySC 5e2zC 5e32C 5e34C 5e35C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 6 molecules CAEDBF
#1: Protein | Mass: 37701.578 Da / Num. of mol.: 3 / Fragment: UNP residues 17-345 / Mutation: Q226L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/duck/Egypt/10185SS/2010(H5N1) / Gene: HA / Plasmid: PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: G8IPF0 #2: Protein | Mass: 20822.039 Da / Num. of mol.: 3 / Fragment: UNP residues 346-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/duck/Egypt/10185SS/2010(H5N1) / Gene: HA / Plasmid: BACULOVIRUS / Details (production host): PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: G8IPF0 |
---|
-Sugars , 4 types, 8 molecules
#3: Polysaccharide | beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
---|---|---|---|---|---|
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
-Non-polymers , 1 types, 160 molecules
#7: Water | ChemComp-HOH / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.03 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.085 M Tris, pH 8.5, 10% (v/v) g;ycerol, 0.17% (w/v) sodium acetate, 21% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03314 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03314 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 52960 / % possible obs: 94.9 % / Redundancy: 2.6 % / Rsym value: 0.07 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.6 / % possible all: 91.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E2Y Resolution: 2.7→49.19 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.98 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|