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Yorodumi- EMDB-42044: H2HA A/Japan/305/1957 complexed with mouse polyclonal Fab - wk 12... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42044 | |||||||||
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Title | H2HA A/Japan/305/1957 complexed with mouse polyclonal Fab - wk 12, reoriented immunogen | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Fab / Hemagglutinin / polyclonal / IMMUNE SYSTEM | |||||||||
Biological species | Influenza A virus (A/Japan/305/1957(H2N2)) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.7 Å | |||||||||
Authors | Carter JJ / Barnes CO | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: Vaccine design via antigen reorientation. Authors: Duo Xu / Joshua J Carter / Chunfeng Li / Ashley Utz / Payton A B Weidenbacher / Shaogeng Tang / Mrinmoy Sanyal / Bali Pulendran / Christopher O Barnes / Peter S Kim / Abstract: A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily ...A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an approach to control antigen orientation via site-specific insertion of aspartate residues that facilitates antigen binding to alum. We demonstrate the generalizability of this approach with antigens from Ebola, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses and observe enhanced neutralizing antibody responses in all cases. We then reorient an H2 HA in an 'upside-down' configuration to increase the exposure and immunogenicity of HA-stem. The reoriented H2 HA (reoH2HA) on alum induced stem-directed antibodies that cross-react with both group 1 and group 2 influenza A subtypes. Electron microscopy polyclonal epitope mapping (EMPEM) revealed that reoH2HA (group 1) elicits cross-reactive antibodies targeting group 2 HA-stems. Our results highlight antigen reorientation as a generalizable approach for designing epitope-focused vaccines. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42044.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-42044-v30.xml emd-42044.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42044_fsc.xml | 3.7 KB | Display | FSC data file |
Images | emd_42044.png | 39.4 KB | ||
Filedesc metadata | emd-42044.cif.gz | 4.8 KB | ||
Others | emd_42044_half_map_1.map.gz emd_42044_half_map_2.map.gz | 2.8 MB 2.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42044 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42044 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42044.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 4.7 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42044_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42044_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : H2HA A/Japan/305/1957 immune complex with mouse polyclonal Fab - ...
Entire | Name: H2HA A/Japan/305/1957 immune complex with mouse polyclonal Fab - week 12, reoriented immunogen group |
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Components |
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-Supramolecule #1: H2HA A/Japan/305/1957 immune complex with mouse polyclonal Fab - ...
Supramolecule | Name: H2HA A/Japan/305/1957 immune complex with mouse polyclonal Fab - week 12, reoriented immunogen group type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Recombinantly expressed H2HA from Polyclonal Fabs generated from pooled reoH2HA-immunized mouse antisera |
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Source (natural) | Organism: Influenza A virus (A/Japan/305/1957(H2N2)) |
-Supramolecule #2: H2HA A/Japan/305/1957
Supramolecule | Name: H2HA A/Japan/305/1957 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #3: Polyclonal Fab
Supramolecule | Name: Polyclonal Fab / type: complex / ID: 3 / Parent: 1 |
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-Macromolecule #1: reoriented H2 HA A/Japan/305/1957
Macromolecule | Name: reoriented H2 HA A/Japan/305/1957 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: MEKIVLLFAI VSLVKSRGDQ ICIGYHANNS TEKVDTILER NVTVTHAKDI LEKTHNGKLC KLNGIPPLEL GDCSIAGWLL GNPECDRLLS VPEWSYIMEK ENPRDGLCFP GSFNDYEELK YLLSSVKHFE KVKILPKDRW TQHTTTGGSR ACAVSGNPSF FRNMVWLTKK ...String: MEKIVLLFAI VSLVKSRGDQ ICIGYHANNS TEKVDTILER NVTVTHAKDI LEKTHNGKLC KLNGIPPLEL GDCSIAGWLL GNPECDRLLS VPEWSYIMEK ENPRDGLCFP GSFNDYEELK YLLSSVKHFE KVKILPKDRW TQHTTTGGSR ACAVSGNPSF FRNMVWLTKK GSDYPVAKGS YNNTSGEQML IIWGVHHPND ETEQRTLYQN VGTYVSVGTS TLNKRSTPEI ATRPKVNGLG SRMEFSWTLL DMWDTINFES TGNLIAPEYG FKISKRGSSG IMKTEGTLEN CETKCQTPLG AINTTLPFHN VHPLTIGECP RYVKSEKLVL ATGLRNVPQI ESRGLFGAIA GFIEGGWQGM VDGWYGYHHS NDQGSGYAAD KESTQKAFDG ITNKVNSVIE KMNTQFEAVG KEFSNLERRL ENLNKKMEDG FLDVWTYNAE LLVLMENERT LDFHDSNVKN LYDKVRMQLR DNVKELGNGC FEFYHKCDDE CMNSVKNGTY DYPKYEEESK LNRNEGSMKQ IEDKIEEILS KIYHIENEIA RIKKLIGEVA SSSGLNDIFE AQKIEWHEAH HHHHHG |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.015 mg/mL |
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Buffer | pH: 7 |
Staining | Type: NEGATIVE / Material: Uranyl Formate |
Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 15.0 e/Å2 |