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Yorodumi- PDB-4hlz: Crystal Structure of Fab C179 in Complex with a H2N2 influenza vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hlz | |||||||||
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Title | Crystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / neutralizing antibodies / antibody affinity / antigens / epitopes / glycosylation / hemagglutinin glycoproteins / immunoglobulin Fab fragments / H2N2 subtype / influenza vaccines / avian flu / envelope protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Dreyfus, C. / Wilson, I.A. | |||||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Structure of a classical broadly neutralizing stem antibody in complex with a pandemic h2 influenza virus hemagglutinin. Authors: Dreyfus, C. / Ekiert, D.C. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hlz.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4hlz.ent.gz | 923.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hlz ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hlz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36504.227 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7S226 #2: Protein | Mass: 20139.295 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7S226 |
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-Antibody , 2 types, 6 molecules GIKHJL
#3: Antibody | Mass: 24853.799 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) #4: Antibody | Mass: 23479.924 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) |
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-Sugars , 4 types, 10 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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 #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 8 molecules
#9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-EDO / | |
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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: 3.56 Å3/Da / Density % sol: 65.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 100115 / Num. obs: 100115 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.9→2.97 Å / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.552 Å / SU ML: 1.19 / σ(F): 1.33 / Phase error: 33.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.834 Å2 / ksol: 0.316 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→39.552 Å
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Refine LS restraints |
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LS refinement shell |
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