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- EMDB-41465: H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05 -
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Open data
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Basic information
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Title | H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05 | ||||||||||||
![]() | H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05 | ||||||||||||
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![]() | influenza / hemagglutinin / monoclonal antibody / immune complex / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Yang YR / Han J / Perrett HR / Ward AB | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita ...Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita Chopde / Masaru Kanekiyo / Katherine V Houser / Grace L Chen / Adrian B McDermott / Sarah F Andrews / Andrew B Ward / ![]() ![]() Abstract: Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in ...Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 118.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 120.8 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 59.9 MB 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tp3MC ![]() 8tp2C ![]() 8tp4C ![]() 8tp5C ![]() 8tp6C ![]() 8tp7C ![]() 8tp9C ![]() 8tpaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Additional Map
File | emd_41465_additional_1.map | ||||||||||||
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Annotation | Additional Map | ||||||||||||
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-Half map: Half Map 1
File | emd_41465_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
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-Half map: Half Map 2
File | emd_41465_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : H1 hemagglutinin (NC99) in complex with Sa-targeting Fab 1-1-1F05
Entire | Name: H1 hemagglutinin (NC99) in complex with Sa-targeting Fab 1-1-1F05 |
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Components |
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-Supramolecule #1: H1 hemagglutinin (NC99) in complex with Sa-targeting Fab 1-1-1F05
Supramolecule | Name: H1 hemagglutinin (NC99) in complex with Sa-targeting Fab 1-1-1F05 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Hemagglutinin HA1 chain
Macromolecule | Name: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 38.289207 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT ...String: MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT GKNGLYPNLS KSYVNNKEKE VLVLWGVHHP PNIGNQRALY HTENAYVSVV SSHYSRRFTP EIAKRPKVRD QE GRINYYW TLLEPGDTII FEANGNLIAP WYAFALSRGF GSGIITSNAP MDECDAKCQT PQGAINSSLP FQNVHPVTIG ECP KYVRSA KLRMVTGLRN IPSIQSR UniProtKB: Hemagglutinin |
-Macromolecule #2: Hemagglutinin HA2 chain
Macromolecule | Name: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.065277 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY P KYSEESKL ...String: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY P KYSEESKL NREKIDGVKL ESMGVYQILA IYSTVASSLV LLVSLGAISF WMCSNGSLQC RICI UniProtKB: Hemagglutinin |
-Macromolecule #3: Heavy chain of Fab 1-1-1F05
Macromolecule | Name: Heavy chain of Fab 1-1-1F05 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.57907 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLQESGPG LVKPSATLSL TCTLSGGSLS THYWSWIRQP PGKGLEYIGN IHYSGSTNYN PSLRSRVTIS VGTSKNQFSL KLTSVTAAD TAVYYCARDA PYSDFLSGVE TGWFDPWGQG TLVIVSS |
-Macromolecule #4: Light chain of Fab 1-1-1F05
Macromolecule | Name: Light chain of Fab 1-1-1F05 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.564807 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EIVMTQSPAT LSVSPGERAT LSCRASQSVS SNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTD FTLTISSLQS EDFAVYSCQ QYNNWPWTFG QGTKVEIK |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 13 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |