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Yorodumi- EMDB-22096: CryoEM map of Full-length Influenza Hemagglutinin (A/Vietnam/1203... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22096 | |||||||||
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Title | CryoEM map of Full-length Influenza Hemagglutinin (A/Vietnam/1203/2004) in complex with 1C4 Fab Fragment | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Influenza A virus / Macaca fascicularis (crab-eating macaque) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Qiu Y / Zhou Y | |||||||||
Citation | Journal: Sci Transl Med / Year: 2021 Title: Broad neutralization of H1 and H3 viruses by adjuvanted influenza HA stem vaccines in nonhuman primates. Authors: Nicole Darricarrère / Yu Qiu / Masaru Kanekiyo / Adrian Creanga / Rebecca A Gillespie / Syed M Moin / Jacqueline Saleh / Jose Sancho / Te-Hui Chou / Yanfeng Zhou / Ruijun Zhang / Shujia Dai ...Authors: Nicole Darricarrère / Yu Qiu / Masaru Kanekiyo / Adrian Creanga / Rebecca A Gillespie / Syed M Moin / Jacqueline Saleh / Jose Sancho / Te-Hui Chou / Yanfeng Zhou / Ruijun Zhang / Shujia Dai / Anthony Moody / Kevin O Saunders / Michelle C Crank / John R Mascola / Barney S Graham / Chih-Jen Wei / Gary J Nabel / Abstract: Seasonal influenza vaccines confer protection against specific viral strains but have restricted breadth that limits their protective efficacy. The H1 and H3 subtypes of influenza A virus cause most ...Seasonal influenza vaccines confer protection against specific viral strains but have restricted breadth that limits their protective efficacy. The H1 and H3 subtypes of influenza A virus cause most of the seasonal epidemics observed in humans and are the major drivers of influenza A virus-associated mortality. The consequences of pandemic spread of COVID-19 underscore the public health importance of prospective vaccine development. Here, we show that headless hemagglutinin (HA) stabilized-stem immunogens presented on ferritin nanoparticles elicit broadly neutralizing antibody (bnAb) responses to diverse H1 and H3 viruses in nonhuman primates (NHPs) when delivered with a squalene-based oil-in-water emulsion adjuvant, AF03. The neutralization potency and breadth of antibodies isolated from NHPs were comparable to human bnAbs and extended to mismatched heterosubtypic influenza viruses. Although NHPs lack the immunoglobulin germline VH1-69 residues associated with the most prevalent human stem-directed bnAbs, other gene families compensated to generate bnAbs. Isolation and structural analyses of vaccine-induced bnAbs revealed extensive interaction with the fusion peptide on the HA stem, which is essential for viral entry. Antibodies elicited by these headless HA stabilized-stem vaccines neutralized diverse H1 and H3 influenza viruses and shared a mode of recognition analogous to human bnAbs, suggesting that these vaccines have the potential to confer broadly protective immunity against diverse viruses responsible for seasonal and pandemic influenza infections in humans. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22096.map.gz | 25.2 MB | EMDB map data format | |
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Header (meta data) | emd-22096-v30.xml emd-22096.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_22096.png | 57.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22096 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22096 | HTTPS FTP |
-Validation report
Summary document | emd_22096_validation.pdf.gz | 300.9 KB | Display | EMDB validaton report |
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Full document | emd_22096_full_validation.pdf.gz | 300.5 KB | Display | |
Data in XML | emd_22096_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22096 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22096 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22096.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab
Entire | Name: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab |
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Components |
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-Supramolecule #1: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab
Supramolecule | Name: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 336 KDa |
-Supramolecule #2: Hemagglutinin
Supramolecule | Name: Hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Influenza A virus |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: 1C4 Fab
Supramolecule | Name: 1C4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Macaca fascicularis (crab-eating macaque) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Influenza Hemagglutinin (A/Vietnam/1203/2004)
Macromolecule | Name: Influenza Hemagglutinin (A/Vietnam/1203/2004) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEKIVLLFAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KKHNGKLCDL DGVKPLILRD CSVAGWLLGN PMCDEFINVP EWSYIVEKAN PVNDLCYPGD FNDYEELKHL LSRINHFEKI QIIPKSSWSS HEASLGVSSA CPYQGKSSFF RNVVWLIKKN ...String: MEKIVLLFAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KKHNGKLCDL DGVKPLILRD CSVAGWLLGN PMCDEFINVP EWSYIVEKAN PVNDLCYPGD FNDYEELKHL LSRINHFEKI QIIPKSSWSS HEASLGVSSA CPYQGKSSFF RNVVWLIKKN STYPTIKRSY NNTNQEDLLV LWGIHHPNDA AEQTKLYQNP TTYISVGTST LNQRLVPRIA TRSKVNGQSG RMEFFWTILK PNDAINFESN GNFIAPEYAY KIVKKGDSTI MKSELEYGNC NTKCQTPMGA INSSMPFHNI HPLTIGECPK YVKSNRLVLA TGLRNSPQRE RRRKKRGLFG AIAGFIEGGW QGMVDGWYGY HHSNEQGSGY AADKESTQKA IDGVTNKVNS IIDKMNTQFE AVGREFNNLE RRIENLNKKM EDGFLDVWTY NAELLVLMEN ERTLDFHDSN VKNLYDKVRL QLRDNAKELG NGCFEFYHKC DNECMESVRN GTYDYPQYSE EARLKREEIS GVKLESIGIY QILSIYSTVA SSLALAIMVA GLSLWMCSNG SLQCRICI |
-Macromolecule #2: Cyno antibody light chain
Macromolecule | Name: Cyno antibody light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca fascicularis (crab-eating macaque) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDTVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYK ASSLQGGVPS RFSGSGSGSD FTLTISSLQS EDFATYYCQ QYSGRPPTFG QGTKVEIKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASVGDTVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYK ASSLQGGVPS RFSGSGSGSD FTLTISSLQS EDFATYYCQ QYSGRPPTFG QGTKVEIKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTDYQS HNVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #3: Cyno antibody heavy chain
Macromolecule | Name: Cyno antibody heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca fascicularis (crab-eating macaque) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSETLSL TCAVSGGTFS AYYWGWIRQP PGKGLEWIGS ISGGSGSTDY SPSLKSRATI SRDTSKNQFS LKLTSVTAA DTAVYYCVRK YWGDYYANWF DVWGPGVLVT VSSASTKGPS VFPLAPCSRS TSESTAALGC LVKDYFPEPV T VSWNSGSL ...String: QVQLQESGPG LVKPSETLSL TCAVSGGTFS AYYWGWIRQP PGKGLEWIGS ISGGSGSTDY SPSLKSRATI SRDTSKNQFS LKLTSVTAA DTAVYYCVRK YWGDYYANWF DVWGPGVLVT VSSASTKGPS VFPLAPCSRS TSESTAALGC LVKDYFPEPV T VSWNSGSL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYVCNVN HKPSNTKVDK RVEIKTCGGG SKPPT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 506644 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: PROJECTION MATCHING |