+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42149 | ||||||||||||
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Title | S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004 | ||||||||||||
Map data | CryoEM map of S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004 | ||||||||||||
Sample |
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Keywords | immunoglobulin / complex / hemagglutinin / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | Function and homology information viral budding from plasma membrane / endocytosis involved in viral entry into 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 | Influenza B virus (B/Malaysia/2506/2004) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.98 Å | ||||||||||||
Authors | Finney J / Kong S / Walsh Jr RM / Harrison SC / Kelsoe G | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Protective human antibodies against a conserved epitope in pre- and postfusion influenza hemagglutinin. Authors: Joel Finney / Annie Park Moseman / Susan Kong / Akiko Watanabe / Shengli Song / Richard M Walsh / Masayuki Kuraoka / Ryutaro Kotaki / E Ashley Moseman / Kevin R McCarthy / Dongmei Liao / ...Authors: Joel Finney / Annie Park Moseman / Susan Kong / Akiko Watanabe / Shengli Song / Richard M Walsh / Masayuki Kuraoka / Ryutaro Kotaki / E Ashley Moseman / Kevin R McCarthy / Dongmei Liao / Xiaoe Liang / Xiaoyan Nie / Olivia Lavidor / Richard Abbott / Stephen C Harrison / Garnett Kelsoe / Abstract: Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both ...Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both IAV and IBV hemagglutinins (HAs) could protect against disease by diverse virus subtypes. Only one reported HA Ab, isolated from a combinatorial display library, protects against both IAV and IBV. Thus, there has been so far no information on the likelihood of finding naturally occurring human Abs that bind HAs of diverse IAV subtypes and IBV lineages. We have now recovered from several unrelated human donors five clonal Abs that bind a conserved epitope preferentially exposed in the postfusion conformation of IAV and IVB HA2. These Abs lack neutralizing activity in vitro but in mice provide strong, IgG subtype-dependent protection against lethal IAV and IBV infections. Strategies to elicit similar Abs routinely might contribute to more effective influenza vaccines. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42149.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-42149-v30.xml emd-42149.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42149_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_42149.png | 63.5 KB | ||
Filedesc metadata | emd-42149.cif.gz | 6.3 KB | ||
Others | emd_42149_half_map_1.map.gz emd_42149_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42149 | HTTPS FTP |
-Validation report
Summary document | emd_42149_validation.pdf.gz | 839.6 KB | Display | EMDB validaton report |
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Full document | emd_42149_full_validation.pdf.gz | 839.1 KB | Display | |
Data in XML | emd_42149_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_42149_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42149 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42149 | HTTPS FTP |
-Related structure data
Related structure data | 8udgMC 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_42149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.54688 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: cryoEM Half-map A
File | emd_42149_half_map_1.map | ||||||||||||
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Annotation | cryoEM Half-map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryoEM Half-map B
File | emd_42149_half_map_2.map | ||||||||||||
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Annotation | cryoEM Half-map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of two S1V2-72 Fabs with postfusion HA2
Entire | Name: Complex of two S1V2-72 Fabs with postfusion HA2 |
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Components |
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-Supramolecule #1: Complex of two S1V2-72 Fabs with postfusion HA2
Supramolecule | Name: Complex of two S1V2-72 Fabs with postfusion HA2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1 Details: Fab fragment generated by proteolytic cleavage of S1V2-72 IgG |
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Source (natural) | Organism: Influenza B virus (B/Malaysia/2506/2004) |
-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 B virus (B/Malaysia/2506/2004) |
Molecular weight | Theoretical: 17.16916 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GYTSHGAHGV AVAADLKSTQ EAINKITKNL NSLSELEVKN LQRLSGAMDE IHNEILELDE KVDDLRADTI SSQIELAVLL SNEGIINSE DEHLLALERK LKKMLGPSAV DIGNGCFETK HKCNQTCLDR IAAGTFNAGE FSLPTFDSLN ITAASLNDDG UniProtKB: Hemagglutinin |
-Macromolecule #2: S1V2-72 heavy chain
Macromolecule | Name: S1V2-72 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: 24.135121 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE LKKPGASVKV SCKASGYTFT GNYIHWMRQV PGQGLEWMGW INPRTGDTHH AQKFQGRVDM TRDTSINTAY LELTRLESD DTALYYCARC VFATSQFDPW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String: QVQLVQSGAE LKKPGASVKV SCKASGYTFT GNYIHWMRQV PGQGLEWMGW INPRTGDTHH AQKFQGRVDM TRDTSINTAY LELTRLESD DTALYYCARC VFATSQFDPW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSCDK |
-Macromolecule #3: S1V2-72 light chain
Macromolecule | Name: S1V2-72 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: 22.755045 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSALTQPASV SGSPGQSITI SCTGTNSDIG SHNLVSWYQQ HPGKAPKVMI YDDSKRPSGV SNRFSGSKSG STASLTISGL QSEDEADYY CCSYAGSSNW VFGGGTKLTL LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String: QSALTQPASV SGSPGQSITI SCTGTNSDIG SHNLVSWYQQ HPGKAPKVMI YDDSKRPSGV SNRFSGSKSG STASLTISGL QSEDEADYY CCSYAGSSNW VFGGGTKLTL LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / 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) / Average electron dose: 76.12 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8udg: |