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Yorodumi- PDB-4yy1: The structure of hemagglutinin from a H6N1 influenza virus (A/chi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yy1 | ||||||||||||||||||
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Title | The structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013) in complex with human receptor analog 6'SLNLN | ||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Hemagglutinin | ||||||||||||||||||
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 | unidentified influenza virus | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Wang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: To Be Published Title: Structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013) Authors: Wang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yy1.cif.gz | 397.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yy1.ent.gz | 334.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yy1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4yy1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4yy1_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 4yy1_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/4yy1 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yy1 | 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
#1: Protein | Mass: 36474.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A0J9X268*PLUS #2: Protein | Mass: 18793.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A0J9X267*PLUS #3: Polysaccharide | #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.15 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium thiocyanate, 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.096→50 Å / Num. obs: 23294 / % possible obs: 92.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.5 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.54 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 30.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→45.54 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 80.3233 Å / Origin y: 85.0313 Å / Origin z: 7.7716 Å
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Refinement TLS group | Selection details: ALL |