[English] 日本語
![](img/lk-miru.gif)
- PDB-5xlc: The structure of hemagglutinin Q226L-G228S mutant from an avian-o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xlc | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 influenza virus in complex with avian receptor analog LSTa | ||||||
![]() | (Hemagglutinin) x 2 | ||||||
![]() | VIRAL PROTEIN / H4 hemagglutinin / influenza virus / receptor binding | ||||||
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 / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, H. / Qi, J. / Gao, G.F. | ||||||
![]() | ![]() Title: Avian-to-Human Receptor-Binding Adaptation by Influenza A Virus Hemagglutinin H4 Authors: Song, H. / Qi, J. / Xiao, H. / Bi, Y. / Zhang, W. / Xu, Y. / Wang, F. / Shi, Y. / Gao, G.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 402.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 334.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.5 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xl1C ![]() 5xl2C ![]() 5xl3C ![]() 5xl4C ![]() 5xl5C ![]() 5xl6C ![]() 5xl7C ![]() 5xl8C ![]() 5xl9C ![]() 5xlaC ![]() 5xlbC ![]() 5xldC ![]() 1ha0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 35981.516 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343 / Mutation: Q226L, G228S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: ![]() #2: Protein | Mass: 20342.391 Da / Num. of mol.: 2 / Fragment: UNP residues 344-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: ![]() #3: Sugar | ChemComp-NAG / #4: Sugar | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.26 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES monohydrate (pH 6.0) and 14% (w/v) PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 53010 / % possible obs: 99.9 % / Redundancy: 9.6 % / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.76 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1HA0 Resolution: 2.4→48.974 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.38
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→48.974 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -255.7039 Å / Origin y: 289.3271 Å / Origin z: -625.6223 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |