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Yorodumi- EMDB-5731: Antibody Recognition of the Pandemic H1N1 Influenza Hemagglutinin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5731 | |||||||||
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Title | Antibody Recognition of the Pandemic H1N1 Influenza Hemagglutinin Receptor Binding Site | |||||||||
Map data | Influenza hemagglutinin (A/Singapore/6/1986, H1N1) bound to neutralizing antibody (Fab 5J8) | |||||||||
Sample |
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Keywords | influenza / hemagglutinin / antibody / neutralizing / Fab | |||||||||
Biological species | Homo sapiens (human) / Influenza A virus | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.0 Å | |||||||||
Authors | Hong M / Lee PS / Hoffman RMB / Zhu X / Krause JC / Laursen NS / Yoon S / Song L / Tussey L / Crowe Jr JE ...Hong M / Lee PS / Hoffman RMB / Zhu X / Krause JC / Laursen NS / Yoon S / Song L / Tussey L / Crowe Jr JE / Ward AB / Wilson IA | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: Antibody recognition of the pandemic H1N1 Influenza virus hemagglutinin receptor binding site. Authors: Minsun Hong / Peter S Lee / Ryan M B Hoffman / Xueyong Zhu / Jens C Krause / Nick S Laursen / Sung-Il Yoon / Langzhou Song / Lynda Tussey / James E Crowe / Andrew B Ward / Ian A Wilson Abstract: Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in ...Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918 and 2009 pandemic viruses. Here, we present the crystal structure of 5J8 Fab in complex with a bacterially expressed and refolded globular head domain from the hemagglutinin (HA) of the A/California/07/2009 (H1N1) pandemic virus. 5J8 recognizes a conserved epitope in and around the receptor binding site (RBS), and its HCDR3 closely mimics interactions of the sialic acid receptor. Electron microscopy (EM) reconstructions of 5J8 Fab in complex with an HA trimer from a 1986 H1 strain and with an engineered stabilized HA trimer from the 2009 H1 pandemic virus showed a similar mode of binding. As for other characterized RBS-targeted antibodies, 5J8 uses avidity to extend its breadth and affinity against divergent H1 strains. 5J8 selectively interacts with HA insertion residue 133a, which is conserved in pandemic H1 strains and has precluded binding of other RBS-targeted antibodies. Thus, the RBS of divergent HAs is targeted by 5J8 and adds to the growing arsenal of common recognition motifs for design of therapeutics and vaccines. Moreover, consistent with previous studies, the bacterially expressed H1 HA properly refolds, retaining its antigenic structure, and presents a low-cost and rapid alternative for engineering and manufacturing candidate flu vaccines. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5731.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-5731-v30.xml emd-5731.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_5731_1.png | 37.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5731 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5731 | HTTPS FTP |
-Validation report
Summary document | emd_5731_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_5731_full_validation.pdf.gz | 78.2 KB | Display | |
Data in XML | emd_5731_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5731 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5731 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5731.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Influenza hemagglutinin (A/Singapore/6/1986, H1N1) bound to neutralizing antibody (Fab 5J8) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Influenza hemagglutinin (A/Singapore/6/1986, H1N1) bound to neutr...
Entire | Name: Influenza hemagglutinin (A/Singapore/6/1986, H1N1) bound to neutralizing antibody (Fab 5J8) |
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Components |
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-Supramolecule #1000: Influenza hemagglutinin (A/Singapore/6/1986, H1N1) bound to neutr...
Supramolecule | Name: Influenza hemagglutinin (A/Singapore/6/1986, H1N1) bound to neutralizing antibody (Fab 5J8) type: sample / ID: 1000 / Oligomeric state: One HA trimer bound to three Fabs / Number unique components: 2 |
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Molecular weight | Theoretical: 289 KDa |
-Macromolecule #1: 5J8 Fab fragment
Macromolecule | Name: 5J8 Fab fragment / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 46 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac Dual |
-Macromolecule #2: Influenza A/Singapore/6/1986 (H1N1) hemagglutinin
Macromolecule | Name: Influenza A/Singapore/6/1986 (H1N1) hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Influenza A virus / Strain: A/Singapore/6/1986 (H1N1) / synonym: Flu |
Molecular weight | Theoretical: 151 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET24a |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.4 / Details: 150 mM NaCl, 50 mM Tris |
Staining | Type: NEGATIVE Details: two cycles of "Nano-W" (2% methylamine tungstate) applied for 20 seconds |
Grid | Details: 400 mesh copper grids coated in nitrocellulose and thin carbon, glow discharged in argon/oxygen |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Average: 298 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism corrected at 100,000 times magnification. |
Date | Feb 14, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 306 Details: Tilt series varying from 0-55 degrees, alternating low and high tilts on similarly stained regions |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55 |
-Image processing
Details | Particles were selected using automatic (difference-of-Gaussians) picking followed by reference-free classification to eliminate noisy picks or non-target aggregation states. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: Appion, Spider, Xmipp, Eman1 / Number images used: 5106 |
Final angle assignment | Details: Eman1: 5 degrees |