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Yorodumi- PDB-4mhj: Crystal structure of Fab H5M9 in complex with influenza virus hem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mhj | |||||||||
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Title | Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/goose/Guangdong/1/96 (H5N1) | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / H5N1 influenza virus / epitope / broadly neutralizing antibody / 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 / 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 / membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.98 Å | |||||||||
Authors | Zhu, X. / Wilson, I.A. | |||||||||
Citation | Journal: J.Virol. / Year: 2013 Title: A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin. Authors: Zhu, X. / Guo, Y.H. / Jiang, T. / Wang, Y.D. / Chan, K.H. / Li, X.F. / Yu, W. / McBride, R. / Paulson, J.C. / Yuen, K.Y. / Qin, C.F. / Che, X.Y. / 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 | 4mhj.cif.gz | 936.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mhj.ent.gz | 753.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mhj_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 4mhj_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4mhj_validation.xml.gz | 181.2 KB | Display | |
Data in CIF | 4mhj_validation.cif.gz | 239 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mhj ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mhj | HTTPS FTP |
-Related structure data
Related structure data | 4mhhC 4mhiSC 3gbmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
-Hemagglutinin ... , 2 types, 12 molecules ACGMOSBDNPIU
#1: Protein | Mass: 37812.707 Da / Num. of mol.: 6 / Fragment: receptor binding domain (UNP residues 17-346) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9Q0U6 #2: Protein | Mass: 20894.012 Da / Num. of mol.: 6 / Fragment: membrane fusion domain (UNP residues 347-521) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9Q0U6 |
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-Antibody , 2 types, 12 molecules LEJXQVHFKTRW
#3: Antibody | Mass: 24049.486 Da / Num. of mol.: 6 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) #4: Antibody | Mass: 23935.797 Da / Num. of mol.: 6 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
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-Sugars , 6 types, 14 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-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: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 #9: 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 #10: 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: 4.19 Å3/Da / Density % sol: 70.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 2% PEG400, 2.0 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2010 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 6.979→174.078 Å / Num. obs: 16538 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.14 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 6.979→7.44 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.92 / % possible all: 64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3GBM AND 4MHI Resolution: 6.98→50.08 Å / Cor.coef. Fo:Fc: 0.759 / Cor.coef. Fo:Fc free: 0.792 / SU B: 0.008 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 4.762 / ESU R Free: 4.646 / 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: 89.86 Å2
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Refinement step | Cycle: LAST / Resolution: 6.98→50.08 Å
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LS refinement shell | Resolution: 6.98→7.16 Å / Total num. of bins used: 20
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