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Yorodumi- EMDB-42056: H7N9 A/Shanghai/2/2013 complexed with mouse polyclonal Fab - wk 7... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42056 | |||||||||
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Title | H7N9 A/Shanghai/2/2013 complexed with mouse polyclonal Fab - wk 7, reoriented immunogen | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Fab / Hemagglutinin / polyclonal / IMMUNE SYSTEM | |||||||||
Biological species | H7N9 subtype (virus) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.5 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_42056.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-42056-v30.xml emd-42056.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42056_fsc.xml | 3.7 KB | Display | FSC data file |
Images | emd_42056.png | 17.5 KB | ||
Filedesc metadata | emd-42056.cif.gz | 5.1 KB | ||
Others | emd_42056_half_map_1.map.gz emd_42056_half_map_2.map.gz | 3.5 MB 3.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42056 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42056 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42056.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
-Sample components
-Entire : H7HA A/Shanghai/2/2013 immune complex with mouse polyclonal Fab -...
Entire | Name: H7HA A/Shanghai/2/2013 immune complex with mouse polyclonal Fab - week 7, reoriented immunogen group |
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Components |
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-Supramolecule #1: H7HA A/Shanghai/2/2013 immune complex with mouse polyclonal Fab -...
Supramolecule | Name: H7HA A/Shanghai/2/2013 immune complex with mouse polyclonal Fab - week 7, reoriented immunogen group type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Recombinantly expressed H7HA with polyclonal Fabs generated from pooled reoH2HA-immunized mouse antisera |
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-Supramolecule #2: H7N9 A/Shanghai/2/2013
Supramolecule | Name: H7N9 A/Shanghai/2/2013 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: H7N9 subtype (virus) |
-Supramolecule #3: Polyclonal Fab
Supramolecule | Name: Polyclonal Fab / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: H7N9 A/Shanghai/2/2013
Macromolecule | Name: H7N9 A/Shanghai/2/2013 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: H7N9 subtype (virus) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLEF SADLIIERRE GSDVCFPGKF VNEEALRQIL RESGGIDKEA MGFTYSGIRT NGATSACRRS GSSFYAEMKW LLSNTDNAAF ...String: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLEF SADLIIERRE GSDVCFPGKF VNEEALRQIL RESGGIDKEA MGFTYSGIRT NGATSACRRS GSSFYAEMKW LLSNTDNAAF PQMTKSYKNT RKSPALIVWG IHHSVSTAEQ TKLYGSGNKL VTVGSSNYQQ SFVPSPGARP QVNGLSGRID FHWLMLNPND TVTFSFNGAF IAPDRASFLR GKSMGIQSGV QVDANCEGDC YHSGGTIISN LPFQNIDSRA VGKCPRYVKQ RSLLLATGMK NVPEIPKGRG LFGAIAGFIE NGWEGLIDGW YGFRHQNAQG EGTAADYKST QSAIDQITGK LNRLIEKTNQ QFELIDNEFN EVEKQIGNVI NWTRDSITEV WSYNAELLVA MENQHTIDLA DSEMDKLYER VKRQLRENAE EDGTGCFEIF HKCDDDCMAS IRNNTYDHSK YREEAMQNRI QIDGSMKQIE DKIEEILSKI YHIENEIARI KKLIGEVASS SGLNDIFEAQ KIEWHEAHHH HHHG |
-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 |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |