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Yorodumi- EMDB-43008: Fab fragment of human mAb #58 in complex with computationally opt... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43008 | |||||||||
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Title | Fab fragment of human mAb #58 in complex with computationally optimized broadly reactive H1 influenza hemagglutinin X6 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / antibody / hemagglutinin / 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 / apical plasma membrane / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Influenza A virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||
Authors | Nagashima KA / Mousa JJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2024 Title: Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6. Authors: Kaito A Nagashima / John V Dzimianski / Meng Yang / Jan Abendroth / Giuseppe A Sautto / Ted M Ross / Rebecca M DuBois / Thomas E Edwards / Jarrod J Mousa / Abstract: Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been ...Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been previously applied to hemagglutinin (HA). This approach integrates wild-type HA sequences into a single immunogen to expand the breadth of accessible antibody epitopes. Adding to previous studies of H1, H3, and H5 COBRA HAs, we define the structural features of another H1 subtype COBRA, X6, that incorporates HA sequences from before and after the 2009 H1N1 influenza pandemic. We determined structures of this antigen alone and in complex with COBRA-specific as well as broadly reactive and functional antibodies, analyzing its antigenicity. We found that X6 possesses features representing both historic and recent H1 HA strains, enabling binding to both head- and stem-reactive antibodies. Overall, these data confirm the integrity of broadly reactive antibody epitopes of X6 and contribute to design efforts for a next-generation vaccine. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43008.map.gz | 417.1 MB | EMDB map data format | |
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Header (meta data) | emd-43008-v30.xml emd-43008.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_43008.png | 57.5 KB | ||
Filedesc metadata | emd-43008.cif.gz | 5.8 KB | ||
Others | emd_43008_additional_1.map.gz emd_43008_half_map_1.map.gz emd_43008_half_map_2.map.gz | 405.6 MB 764.8 MB 764.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43008 | HTTPS FTP |
-Validation report
Summary document | emd_43008_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_43008_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_43008_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_43008_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43008 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43008 | HTTPS FTP |
-Related structure data
Related structure data | 8v7oMC 8f38C 8ghkC 8sj9C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43008.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.526 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_43008_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43008_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43008_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of COBRA HA X6 with #58 Fab
Entire | Name: Complex of COBRA HA X6 with #58 Fab |
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Components |
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-Supramolecule #1: Complex of COBRA HA X6 with #58 Fab
Supramolecule | Name: Complex of COBRA HA X6 with #58 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 62.494656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCLLKGIAPL QLGNCSVAGW ILGNPECELL ISKESWSYIV ETPNPENGT CYPGYFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTVT GVSASCSHNG KSSFYRNLLW LTGKNGLYPN L SKSYANNK ...String: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCLLKGIAPL QLGNCSVAGW ILGNPECELL ISKESWSYIV ETPNPENGT CYPGYFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTVT GVSASCSHNG KSSFYRNLLW LTGKNGLYPN L SKSYANNK EKEVLVLWGV HHPPNIGDQR ALYHTENAYV SVVSSHYSRK FTPEIAKRPK VRDQEGRINY YWTLLEPGDT II FEANGNL IAPRYAFALS RGFGSGIITS NAPMDECDAK CQTPQGAINS SLPFQNVHPV TIGECPKYVR SAKLRMVTGL RNI PSIQSR GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLE RRMEN LNKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKN GTYD YPKYSEESKL NREKIDGVGT GYIPEAPRDG QAYVRKDGEW VLLSTFLGSG LNDIFEAQKI EWHEGHHHHH H UniProtKB: Hemagglutinin |
-Macromolecule #2: #58 heavy chain
Macromolecule | Name: #58 heavy chain / type: protein_or_peptide / ID: 2 Details: Heavy chain Fab fragment variable region of human mAb #58 Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.052598 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSETLSL TCNVSGGSIN SYYWSWIRQP PGKGLEWIGY VYHSGSTHYN PSLNSRVTIS VDTSKRQFSL KLRSVTAAD TAVYYCAREK SDFWTVDSFF YYMDVWGRGT TVTVSS |
-Macromolecule #3: #58 light chain
Macromolecule | Name: #58 light chain / type: protein_or_peptide / ID: 3 Details: Kappa chain Fab fragment variable region of human mAb #58 Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.797213 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPAT LSLSPGERAT LSCRASQSVA TSLAWYQQKP GQPPRLLIYD ASHRATAIPA RFTGSGSGTD FTLTISSLEP EDFAVYYCQ QRTHWPPALT FGGGTKVEIK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 57.22 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110051 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |