[English] 日本語
![](img/lk-miru.gif)
- PDB-6e7g: Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Na... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6e7g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus | |||||||||
![]() |
| |||||||||
![]() | VIRAL PROTEIN / Influenza virus / hemagglutinin / HA / H5N1 / A/Viet Nam/1203/2004 / Receptor specificity | |||||||||
Function / homology | ![]() 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 ...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 / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tzarum, N. / Wilson, I.A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses. Authors: Broszeit, F. / Tzarum, N. / Zhu, X. / Nemanichvili, N. / Eggink, D. / Leenders, T. / Li, Z. / Liu, L. / Wolfert, M.A. / Papanikolaou, A. / Martinez-Romero, C. / Gagarinov, I.A. / Yu, W. / ...Authors: Broszeit, F. / Tzarum, N. / Zhu, X. / Nemanichvili, N. / Eggink, D. / Leenders, T. / Li, Z. / Liu, L. / Wolfert, M.A. / Papanikolaou, A. / Martinez-Romero, C. / Gagarinov, I.A. / Yu, W. / Garcia-Sastre, A. / Wennekes, T. / Okamatsu, M. / Verheije, M.H. / Wilson, I.A. / Boons, G.J. / de Vries, R.P. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 297.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 239.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6e7hC ![]() 6n5aC ![]() 2fkoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37855.922 Da / Num. of mol.: 3 / Mutation: Y161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: ![]() #2: Protein | Mass: 20414.504 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: ![]() #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.06 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 3350, 0.1M Na-Acetate, pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97962 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 38317 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.91 / Rpim(I) all: 0.07 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3.1→3.15 Å / CC1/2: 0.57 / Rpim(I) all: 0.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2FKO Resolution: 3.094→37.814 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.81 / 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: 3.094→37.814 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|