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Yorodumi- PDB-7scn: Structure of H1 NC99 influenza hemagglutinin bound to Fab 310-63E6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7scn | |||||||||
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Title | Structure of H1 NC99 influenza hemagglutinin bound to Fab 310-63E6 | |||||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / hemagglutinin / influenza / antibody / VIRAL 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 / 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 Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
Authors | Ward, A. / Torrents de la Pena, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Immunity / Year: 2022 Title: Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus. Authors: Maya Sangesland / Alba Torrents de la Peña / Seyhan Boyoglu-Barnum / Larance Ronsard / Faez Amokrane Nait Mohamed / Thalia Bracamonte Moreno / Ralston M Barnes / Daniel Rohrer / Nils ...Authors: Maya Sangesland / Alba Torrents de la Peña / Seyhan Boyoglu-Barnum / Larance Ronsard / Faez Amokrane Nait Mohamed / Thalia Bracamonte Moreno / Ralston M Barnes / Daniel Rohrer / Nils Lonberg / Musie Ghebremichael / Masaru Kanekiyo / Andrew Ward / Daniel Lingwood / Abstract: Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) ...Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) within their CDRH2 loops. Despite this, we demonstrated that both alleles encode for human IAV bnAbs that employ structurally convergent modes of contact to the same epitope. To resolve differences in lineage expandability, we compared F54 versus L54 as substrate within humanized mice, where antibodies develop with human-like CDRH3 diversity but are restricted to single V genes. While both alleles encoded for bnAb precursors, only F54 IGHV1-69 supported elicitation of heterosubtypic serum bnAbs following immunization with a stalk-only nanoparticle vaccine. L54 IGHV1-69 was unproductive, co-encoding for anergic B cells and autoreactive stalk antibodies that were cleared from B cell memory. Moreover, human stalk antibodies also demonstrated L54-dependent autoreactivity. Therefore, IGHV1-69 polymorphism, which is skewed ethnically, gates tolerance and vaccine expandability of influenza bnAbs. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7scn.cif.gz | 418.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7scn.ent.gz | 345.8 KB | Display | PDB format |
PDBx/mmJSON format | 7scn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/7scn ftp://data.pdbj.org/pub/pdb/validation_reports/sc/7scn | HTTPS FTP |
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-Related structure data
Related structure data | 25039MC 7scoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35932.309 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1) Strain: A/New Zealand:South Canterbury/35/2000 H1N1 / Gene: HA / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q289M7 #2: Protein | Mass: 26637.555 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1) Strain: A/New Zealand:South Canterbury/35/2000 H1N1 / Gene: HA / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q289M7 #3: Antibody | Mass: 13394.064 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human) #4: Antibody | Mass: 11810.081 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293F / Cell line (production host): 293F / Production host: Homo sapiens (human) #5: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Structure of H1 NC99 influenza hemagglutinin bound to 310-63E6 Fab Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Influenza A virus | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: 293F | |||||||||||||||
Buffer solution | pH: 7.4 / Details: TBS buffer, PH 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: hemagglutinin at 2 mg/ml is complexed with the Fab at a molar ratio 1:3 (HA:Fab). The sample is incubated for 30min at RT and diluted with TBS to a final concentration of 0.2 mg/ml | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K Details: Blotting time: 5.5 s Blotting force: 0 Waiting time: 7 s |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Average exposure time: 10 sec. / Electron dose: 49.88 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 958 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123683 / Algorithm: BACK PROJECTION / Symmetry type: POINT |