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Yorodumi- PDB-5tr8: Crystal structure of vaccine-elicited pan- influenza H1N1 neutral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tr8 | ||||||
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Title | Crystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Nanoparticle / Ferritin / Antibody | ||||||
Function / homology | Function and homology information Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Joyce, M.G. / Kanekiyo, M. / Mascola, J.R. / Graham, B.S. / Kwong, P.D. | ||||||
Citation | Journal: Nat Immunol / Year: 2019 Title: Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits broad B cell responses. Authors: Masaru Kanekiyo / M Gordon Joyce / Rebecca A Gillespie / John R Gallagher / Sarah F Andrews / Hadi M Yassine / Adam K Wheatley / Brian E Fisher / David R Ambrozak / Adrian Creanga / Kwanyee ...Authors: Masaru Kanekiyo / M Gordon Joyce / Rebecca A Gillespie / John R Gallagher / Sarah F Andrews / Hadi M Yassine / Adam K Wheatley / Brian E Fisher / David R Ambrozak / Adrian Creanga / Kwanyee Leung / Eun Sung Yang / Seyhan Boyoglu-Barnum / Ivelin S Georgiev / Yaroslav Tsybovsky / Madhu S Prabhakaran / Hanne Andersen / Wing-Pui Kong / Ulrich Baxa / Kathryn L Zephir / Julie E Ledgerwood / Richard A Koup / Peter D Kwong / Audray K Harris / Adrian B McDermott / John R Mascola / Barney S Graham / Abstract: The present vaccine against influenza virus has the inevitable risk of antigenic discordance between the vaccine and the circulating strains, which diminishes vaccine efficacy. This necessitates new ...The present vaccine against influenza virus has the inevitable risk of antigenic discordance between the vaccine and the circulating strains, which diminishes vaccine efficacy. This necessitates new approaches that provide broader protection against influenza. Here we designed a vaccine using the hypervariable receptor-binding domain (RBD) of viral hemagglutinin displayed on a nanoparticle (np) able to elicit antibody responses that neutralize H1N1 influenza viruses spanning over 90 years. Co-display of RBDs from multiple strains across time, so that the adjacent RBDs are heterotypic, provides an avidity advantage to cross-reactive B cells. Immunization with the mosaic RBD-np elicited broader antibody responses than those induced by an admixture of nanoparticles encompassing the same set of RBDs as separate homotypic arrays. Furthermore, we identified a broadly neutralizing monoclonal antibody in a mouse immunized with mosaic RBD-np. The mosaic antigen array signifies a unique approach that subverts monotypic immunodominance and allows otherwise subdominant cross-reactive B cell responses to emerge. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tr8.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tr8.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 5tr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/5tr8 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/5tr8 | HTTPS FTP |
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-Related structure data
Related structure data | 7021C 4zptS 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
#1: Antibody | Mass: 23694.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) / References: UniProt: Q7TS98 | ||
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#2: Antibody | Mass: 23879.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Homo sapiens (human) / References: UniProt: A0A0E4B366 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.44 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop Details: 12% PEG3350, 100 mM HEPES pH 7.5, 5 mM MgCl2, 5mM NiCl2 |
-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: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.607 Å / Num. obs: 42733 / % possible obs: 98.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.57 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.49 / CC1/2: 0.718 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZPT Resolution: 2.01→24.607 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79 / 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: 2.01→24.607 Å
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Refine LS restraints |
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LS refinement shell |
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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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