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Yorodumi- EMDB-40046: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40046 | |||||||||
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Title | CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NIAID / hemagglutinin stalk binding antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Biological species | Influenza A virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
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_40046.map.gz | 625.6 MB | EMDB map data format | |
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Header (meta data) | emd-40046-v30.xml emd-40046.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40046_fsc.xml | 19.4 KB | Display | FSC data file |
Images | emd_40046.png | 62.9 KB | ||
Filedesc metadata | emd-40046.cif.gz | 6.5 KB | ||
Others | emd_40046_half_map_1.map.gz emd_40046_half_map_2.map.gz | 615.2 MB 615.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40046 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40046 | HTTPS FTP |
-Validation report
Summary document | emd_40046_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_40046_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_40046_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | emd_40046_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40046 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40046 | HTTPS FTP |
-Related structure data
Related structure data | 8ghkMC 8f38C 8sj9C 8v7oC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40046.map.gz / Format: CCP4 / Size: 662.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40046_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40046_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) ...
Entire | Name: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab |
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Components |
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-Supramolecule #1: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) ...
Supramolecule | Name: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 221 KDa |
-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 / Strain: 1/Melbourne/1/1946(H1N1) |
Molecular weight | Theoretical: 53.994246 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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 PSIAGF IEGGWTGMVD GWYGYHHQNE QGSGYAADQK STQNAINGIT NKVNSVIEKM NTQFTAVGKE FNKLERRMEN LNKK VDDGF LDIWTYNAEL LVLLENERTL DFHDSNVKNL YEKVKSQLKN NAKEIGNGCF EFYHKCNNEC MESVKNGTYD YPKYS |
-Macromolecule #2: GS10-X6-BE4 Fab Heavy chain
Macromolecule | Name: GS10-X6-BE4 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.154263 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVLGLKWVFF VVLYQGVHCE VQLVESGGGL VQPKGSLKLS CATSGFTFNT FDMHWVRQAP GKDLEWVARI RTKGNSYATY YAASVKDRI TISRDDSQSM LYLEMNSLRS EDTAMYYCVR EGGHYYGYYF DFWGQGTTLT VSS |
-Macromolecule #3: GS10-X6-BE4 Fab light chain
Macromolecule | Name: GS10-X6-BE4 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.949619 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSSAQFLGLL LLCFQGTRCE IQMTQTTSSL SASLGDRVTI SCRASQDIYN YLNWYQQQPD GAVKLLIYYT SKLHSGVPSR FSGSGSGTD YSLTITNLEQ EDIATYFCQQ GYTLPYTFGG GTKLEIK |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: LACEY | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7031 / Average exposure time: 2.4 sec. / Average electron dose: 80.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |