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Yorodumi- PDB-1jsn: STRUCTURE OF AVIAN H5 HAEMAGGLUTININ COMPLEXED WITH LSTA RECEPTRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jsn | |||||||||
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Title | STRUCTURE OF AVIAN H5 HAEMAGGLUTININ COMPLEXED WITH LSTA RECEPTRO ANALOG | |||||||||
Components | (HAEMAGGLUTININ ...Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / influenza / receptor complex / fusion protein | |||||||||
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: 2.4 Å | |||||||||
Authors | Ha, Y. / Stevens, D.J. / Skehel, J.J. / Wiley, D.C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jsn.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jsn.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1jsn ftp://data.pdbj.org/pub/pdb/validation_reports/js/1jsn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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) Influenza A virus / Genus: Influenzavirus A / Strain: A/Duck/Singapore/3/97 / References: UniProt: A5Z226 |
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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) Influenza A virus / Genus: Influenzavirus A / Strain: A/Duck/Singapore/3/97 / References: UniProt: A5Z226*PLUS |
-Sugars , 3 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 1 types, 216 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.02 % |
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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: 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: 2.4→40 Å / Num. all: 33434 / Num. obs: 27009 / % possible obs: 80.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.4→40 Å / % possible all: 81 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 30623 / % possible obs: 92.7 % / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.709 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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 / Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.634 / Rfactor obs: 0.588 |