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- PDB-1jso: STRUCTURE OF AVIAN H5 HAEMAGGLUTININ BOUND TO LSTC RECEPTOR ANALOG -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jso | |||||||||
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Title | STRUCTURE OF AVIAN H5 HAEMAGGLUTININ BOUND TO LSTC RECEPTOR ANALOG | |||||||||
![]() | (HAEMAGGLUTININ ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / influenza / receptor complex / fusion protein | |||||||||
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 Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ha, Y. / Stevens, D.J. / Skehel, J.J. / Wiley, D.C. | |||||||||
![]() | ![]() Title: X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs. Authors: Ha, Y. / Stevens, D.J. / Skehel, J.J. / Wiley, D.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.6 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 581 KB | Display | ![]() |
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Full document | ![]() | 592.3 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-HAEMAGGLUTININ ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36573.207 Da / Num. of mol.: 1 / Fragment: Residues 1-325 / Source method: isolated from a natural source / Details: AUTO CLEAVED FRAGMENT OF N-TERMINUS / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 20200.232 Da / Num. of mol.: 1 / Fragment: Residues 1-176 / Source method: isolated from a natural source / Details: AUTO CLEAVED FRAGMENT OF C-TERMINUS / Source: (natural) ![]() ![]() |
-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SIA.gif)
![](data/chem/img/SIA.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | ChemComp-SIA / | |
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-Non-polymers , 1 types, 290 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MME-PEG 2000, NICL2, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 31, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 33114 / Num. obs: 29280 / % possible obs: 88.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.4→40 Å / % possible all: 88.4 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 90.6 % / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 87.5 % / Rmerge(I) obs: 0.259 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 40 Å / σ(F): 0 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / Rfactor obs: 0.267 |