+Open data
-Basic information
Entry | Database: PDB / ID: 3m5g | |||||||||
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Title | Crystal structure of a H7 influenza virus hemagglutinin | |||||||||
Components | (Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / influenza virus / hemagglutinin / Envelope protein / Fusion protein / Host cell membrane / Host membrane / Membrane / Transmembrane / Virion | |||||||||
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: 2.6 Å | |||||||||
Authors | Yang, H. / Chen, L.M. / Carney, P.J. / Donis, R.O. / Stevens, J. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: Structures of receptor complexes of a North American H7N2 influenza hemagglutinin with a loop deletion in the receptor binding site. Authors: Yang, H. / Chen, L.M. / Carney, P.J. / Donis, R.O. / Stevens, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m5g.cif.gz | 295.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m5g.ent.gz | 237.9 KB | Display | PDB format |
PDBx/mmJSON format | 3m5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m5g_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3m5g_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3m5g_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 3m5g_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/3m5g ftp://data.pdbj.org/pub/pdb/validation_reports/m5/3m5g | HTTPS FTP |
-Related structure data
Related structure data | 3m5hC 3m5iC 3m5jC 1ti8S 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
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 34880.359 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B7NY59 #2: Protein | Mass: 20895.980 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B7NYS1 |
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-Sugars , 2 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 2 types, 296 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONFLICTS IN THE SEQUENCE IS BECAUSE THE AUTHORS USED THE GENEBANK SEQUENCE ACC55270.1 WHICH IS ...THE CONFLICTS IN THE SEQUENCE IS BECAUSE THE AUTHORS USED THE GENEBANK SEQUENCE ACC55270.1 WHICH IS A SLIGHTLY DIFFERENT STRAIN |
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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: 2.89 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 7.2 Details: 20% PEG 3350, 0.2 M magnesium chloride at pH 7.2, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 62462 / Num. obs: 61857 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rsym value: 0.106 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.413 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1TI8 Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.882 / SU B: 20.843 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.308 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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