[English] 日本語
Yorodumi- EMDB-7021: Structure of influenza hemagglutinin from A/New Caledonia/20/99 i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7021 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of influenza hemagglutinin from A/New Caledonia/20/99 in complex with FAB 441D6. | |||||||||
Map data | Hemagglutinin ectodomain derived from influenza A/New Caledonia/20/99 expressed with a trimerization domain (foldon), in complex with 3 molecules of FAB 441D6. | |||||||||
Sample |
| |||||||||
Biological species | Influenza A virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Gallagher JR / Harris AK | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7021.map.gz | 62.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7021-v30.xml emd-7021.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7021_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_7021.png | 94.4 KB | ||
Masks | emd_7021_msk_1.map | 67 MB | Mask map | |
Others | emd_7021_half_map_1.map.gz emd_7021_half_map_2.map.gz | 51.9 MB 51.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7021 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7021 | HTTPS FTP |
-Validation report
Summary document | emd_7021_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_7021_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_7021_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7021 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7021 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_7021.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Hemagglutinin ectodomain derived from influenza A/New Caledonia/20/99 expressed with a trimerization domain (foldon), in complex with 3 molecules of FAB 441D6. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3797 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_7021_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: RELION unfiltered half map (1)
File | emd_7021_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RELION unfiltered half map (1) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: RELION unfiltered half map (2)
File | emd_7021_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RELION unfiltered half map (2) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Influenza hemagglutinin from A/New Caledonia/20/99, in complex wi...
Entire | Name: Influenza hemagglutinin from A/New Caledonia/20/99, in complex with 3 molecules of FAB 441D6. |
---|---|
Components |
|
-Supramolecule #1: Influenza hemagglutinin from A/New Caledonia/20/99, in complex wi...
Supramolecule | Name: Influenza hemagglutinin from A/New Caledonia/20/99, in complex with 3 molecules of FAB 441D6. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Influenza A virus / Strain: A/New Caledonia/20/99 |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Influenza hemagglutinin from A/New Caledonia/20/99, with C-termin...
Macromolecule | Name: Influenza hemagglutinin from A/New Caledonia/20/99, with C-terminal trimerization domain (T4 fibritin foldon). type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Influenza A virus / Strain: A/New Caledonia/20/99 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGTAPL QLGNCSVAGW ILGNPECESL FSKESWSYIA ETPNPENGTC YPGYFADYEE LREQLSSVSS FERFEIFPKE SSWPNHTVTK GVTASCSHNG KSSFYKNLLW LTEKNGLYPN LSKSYVNNKE ...String: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGTAPL QLGNCSVAGW ILGNPECESL FSKESWSYIA ETPNPENGTC YPGYFADYEE LREQLSSVSS FERFEIFPKE SSWPNHTVTK GVTASCSHNG KSSFYKNLLW LTEKNGLYPN LSKSYVNNKE KEVLVLWGVH HPSNIGDQRA IYHTENAYVS VVSSHYSRRF TPEITKRPKV RDQEGRINYY WTLLEPGDTI IFEANGNLIA PWYAFALSRG FGSGIITSNA SMGECDAKCQ TPQGAINSSL PFQNVHPVTI GECPKYVRST KLRMVTGLRN IPSIQSRGLF GAIAGFIEGG WTGMIDGWYG YHHQNEQGSG YAADQKSTQN AIDGITNKVN SVIEKMNTQF TAVGKEFNKL ERRMENLNKK VDDGFLDIWT YNAELLVLLE NERTLDFHDS NVKNLYEKVK TQLKNNAKEI GNGCFEFYHK CNNECMESVK NGTYDYPKYS EESKLNREKI DGSGLVPRGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGSA HIVMVDAYKP TKGHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
Details: PBS | |||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Complexes of hemagglutinin and FAB were purified from unbound components by gel filtration. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 464 / Average exposure time: 1.0 sec. / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |