+Open data
-Basic information
Entry | Database: PDB / ID: 1jsd | |||||||||
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Title | CRYSTAL STRUCTURE OF SWINE H9 HAEMAGGLUTININ | |||||||||
Components | (HAEMAGGLUTININ ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / influenza | |||||||||
Function / homology | Function and homology information 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 Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | |||||||||
Authors | Ha, Y. / Steven, D.J. / Skehel, J.J. / Wiley, D.C. | |||||||||
Citation | Journal: EMBO J. / Year: 2002 Title: H5 avian and H9 swine influenza virus haemagglutinin structures: possible origin of influenza subtypes. Authors: Ha, Y. / Stevens, D.J. / Skehel, J.J. / Wiley, D.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jsd.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jsd.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jsd_validation.pdf.gz | 633.6 KB | Display | wwPDB validaton report |
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Full document | 1jsd_full_validation.pdf.gz | 640.6 KB | Display | |
Data in XML | 1jsd_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1jsd_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1jsd ftp://data.pdbj.org/pub/pdb/validation_reports/js/1jsd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-HAEMAGGLUTININ ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35456.852 Da / Num. of mol.: 1 / Fragment: Residues 1-319 / Source method: isolated from a natural source / Details: AUTO CLEAVED FRAGMENT OF N-TERMINUS Source: (natural) Influenza A virus (A/swine/Hong Kong/9/98(H9N2)) Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/Swine/Hong Kong/9/98 / References: UniProt: Q91CD4 |
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#2: Protein | Mass: 20038.385 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) Influenza A virus (A/swine/Hong Kong/9/98(H9N2)) Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/Swine/Hong Kong/9/98 / References: UniProt: Q91CD4*PLUS |
-Sugars , 2 types, 5 molecules
#3: 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 #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 283 molecules
#5: Chemical | ChemComp-PO4 / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.08 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: na citrate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
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: 1.8→40 Å / Num. all: 91194 / Num. obs: 91194 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 100 % / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 9090 / Rmerge(I) obs: 0.482 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.332 / Rfactor obs: 0.325 |