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Yorodumi- PDB-6fyw: Structure of B/Brisbane/60/2008 Influenza Hemagglutinin in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fyw | |||||||||
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Title | Structure of B/Brisbane/60/2008 Influenza Hemagglutinin in complex with SD83 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza / single domain antibody / hemagglutinin | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell surface receptor binding / symbiont entry into host cell / 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 ...viral budding from plasma membrane / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell surface receptor binding / symbiont entry into host cell / 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 B virus Lama glama (llama) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Laursen, N.S. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2018 Title: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson / Abstract: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fyw.cif.gz | 251.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fyw.ent.gz | 200.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/6fyw ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fyw | HTTPS FTP |
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-Related structure data
Related structure data | 9029C 6ck8C 6cnvC 6cnwC 6fysC 6fytC 6fyuC 4fqmS S: Starting model for refinement 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37699.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Brisbane/60/2008) / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0LT35 |
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#2: Protein | Mass: 19264.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Brisbane/60/2008) / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0LT35, UniProt: C0LT38*PLUS |
-Antibody , 1 types, 1 molecules C
#3: Antibody | Mass: 13837.263 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: EVQLVESGGGLVQPGGSLRLSCAATGFTLENKAIGWFRQTPGSEREGVLCISKSGSWTYYTDSMRGRFTISRDNAENTVYLQMDSLKPEDTAVYYCATTTAGGGLCWDGTTFSRLASSWGQGTQVTVSS Source: (gene. exp.) Lama glama (llama) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
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-Sugars , 5 types, 6 molecules
#4: 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 | ||||
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#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 | ||||
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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 #8: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 397 molecules
#9: Chemical | ChemComp-GOL / #10: 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: 3.99 Å3/Da / Density % sol: 69.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M MES, pH 6.5 and 10% PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 56754 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 35 Å2 / CC1/2: 1 / Rpim(I) all: 0.06 / Rsym value: 0.13 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.1 % / Num. unique obs: 5669 / CC1/2: 0.62 / Rpim(I) all: 0.44 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FQM Resolution: 2.2→47.26 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.26 Å
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Refine LS restraints |
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LS refinement shell |
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