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Yorodumi- PDB-4fqi: Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fqi | |||||||||
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Title | Crystal Structure of Fab CR9114 in Complex with a H5N1 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 / H5N1 subtype / influenza vaccines / avian flu / envelope protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / identical protein binding Similarity search - Function | |||||||||
Biological species | Influenza A virus Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Dreyfus, C. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 2012 Title: Highly conserved protective epitopes on influenza B viruses. Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt ...Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt / Mohammed Lamrani / Hans J W M Korse / Eric Geelen / Özcan Sahin / Martijn Sieuwerts / Just P J Brakenhoff / Ronald Vogels / Olive T W Li / Leo L M Poon / Malik Peiris / Wouter Koudstaal / Andrew B Ward / Ian A Wilson / Jaap Goudsmit / Robert H E Friesen / Abstract: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. ...Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fqi.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fqi.ent.gz | 179.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fqi_validation.pdf.gz | 845.6 KB | Display | wwPDB validaton report |
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Full document | 4fqi_full_validation.pdf.gz | 857.3 KB | Display | |
Data in XML | 4fqi_validation.xml.gz | 47.8 KB | Display | |
Data in CIF | 4fqi_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/4fqi ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fqi | HTTPS FTP |
-Related structure data
Related structure data | 2143C 2144C 2145C 2146C 2147C 2148C 2149C 2150C 4fqhC 4fqjC 4fqkC 4fqlC 4fqmC 4fqvC 4fqyC C: citing same article (ref.) |
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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
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 37948.020 Da / Num. of mol.: 1 / Fragment: UNP residues 17-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6DQ33 |
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#2: Protein | Mass: 20414.504 Da / Num. of mol.: 1 / Fragment: UNP residues 347-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6DQ33 |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24423.191 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
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#4: Antibody | Mass: 22840.172 Da / Num. of mol.: 1 / Fragment: Fab Lambda Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
-Sugars , 2 types, 4 molecules
#5: 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 |
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#7: Sugar |
-Non-polymers , 3 types, 1103 molecules
#6: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
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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: 3.5 Å3/Da / Density % sol: 64.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.16 M sodium thiocyanate, 15% PEG3350, 100 mM Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 75 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.033 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2011 |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→50 Å / Num. all: 158783 / Num. obs: 158783 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.71→1.74 Å / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→36.553 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 25.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.052 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.71→36.553 Å
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Refine LS restraints |
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LS refinement shell |
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