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Yorodumi- PDB-3htp: the hemagglutinin structure of an avian H1N1 influenza A virus in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3htp | |||||||||
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Title | the hemagglutinin structure of an avian H1N1 influenza A virus in complex with LSTa | |||||||||
Components |
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Keywords | VIRAL PROTEIN / receptor | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.96 Å | |||||||||
Authors | Wang, G. / Li, A. / Zhang, Q. / Wu, C. / Zhang, R. / Cai, Q. / Song, W. / Yuen, K.-Y. | |||||||||
Citation | Journal: Virology / Year: 2009 Title: The hemagglutinin structure of an avian H1N1 influenza A virus Authors: Lin, T. / Wang, G. / Li, A. / Zhang, Q. / Wu, C. / Zhang, R. / Cai, Q. / Song, W. / Yuen, K.-Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3htp.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3htp.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 3htp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/3htp ftp://data.pdbj.org/pub/pdb/validation_reports/ht/3htp | HTTPS FTP |
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-Related structure data
Related structure data | 3htoC 3htqC 3httC 1ru7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 35946.227 Da / Num. of mol.: 1 / Fragment: HA1 chain, UNP residues 15-338 / Source method: isolated from a natural source Source: (natural) Influenza A virus (A/WDK/JX/12416/2005(H1N1)) Strain: WDK/JX/12416/2005 / References: UniProt: C7C6F1 |
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#2: Protein | Mass: 18288.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Influenza A virus (A/WDK/JX/12416/2005(H1N1)) Strain: WDK/JX/12416/2005 / References: UniProt: C7C6F1*PLUS |
-Sugars , 3 types, 4 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#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 |
-Non-polymers , 1 types, 211 molecules
#6: Water | ChemComp-HOH / |
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-Details
Sequence details | THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR CHAIN B AT THE TIME OF PROCESSING |
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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: 6.038052 Å3/Da / Density % sol: 79.629189 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 100mM HEPES pH6.8, 40% PEG 400, 120mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-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 315 / Detector: CCD / Date: Dec 6, 2007 / Details: Bent conical Si-mirror |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→50 Å / Num. obs: 27390 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 42.01 Å2 / Rmerge(I) obs: 0.253 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.96→3.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 6.3 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RU7 Resolution: 2.96→49.71 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso max: 124.29 Å2 / Biso mean: 60.77 Å2 / Biso min: 20.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→49.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.96→2.98 Å / Total num. of bins used: 50
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