+Open data
-Basic information
Entry | Database: PDB / ID: 3m6s | |||||||||
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Title | Crystal structure of H1N1pdm Hemagglutinin | |||||||||
Components | (Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza virus / Hemagglutinin / pandemic / Envelope protein / Fusion protein / Host cell membrane / Host membrane / Membrane / Transmembrane / Virion | |||||||||
Function / homology | Function and homology information clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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: 2.8 Å | |||||||||
Authors | Yang, H. / Carney, P.J. / Stevens, J. | |||||||||
Citation | Journal: PLoS Curr / Year: 2010 Title: Structure and Receptor binding properties of a pandemic H1N1 virus hemagglutinin Authors: Yang, H. / Carney, P. / Stevens, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m6s.cif.gz | 572.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m6s.ent.gz | 473.7 KB | Display | PDB format |
PDBx/mmJSON format | 3m6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/3m6s ftp://data.pdbj.org/pub/pdb/validation_reports/m6/3m6s | HTTPS FTP |
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-Related structure data
Related structure data | 3ku3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Details | The biological unit is a trimer. |
-Components
#1: Protein | Mass: 36661.324 Da / Num. of mol.: 6 / Fragment: Hemagglutinin HA1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Darwin/2001/2009(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5MV42 #2: Protein | Mass: 20759.008 Da / Num. of mol.: 6 / Fragment: Hemagglutinin HA2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Darwin/2001/2009(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5MV42 #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: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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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: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 7.5 Details: 22% PEG2000MME, 0.1M HEPES at pH7.5, microbatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 96521 / Num. obs: 94645 / % possible obs: 98.1 % / Redundancy: 2 % / Rsym value: 0.076 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.442 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KU3 Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.889 / SU B: 36.705 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.604 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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