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Yorodumi- EMDB-41469: H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targetin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41469 | ||||||||||||
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Title | H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targeting Fab 4-1-1G03 | ||||||||||||
Map data | H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targeting Fab 4-1-1G03 | ||||||||||||
Sample |
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Keywords | influenza / hemagglutinin / monoclonal antibody / immune complex / VIRAL PROTEIN / 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 | Influenza A virus (A/Singapore/1/1957(H2N2)) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Yang YR / Han J / Perrett HR / Ward AB | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: bioRxiv / Year: 2023 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 | emd_41469.map.gz | 118.1 MB | EMDB map data format | |
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Header (meta data) | emd-41469-v30.xml emd-41469.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41469_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_41469.png | 138 KB | ||
Masks | emd_41469_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-41469.cif.gz | 6.5 KB | ||
Others | emd_41469_additional_1.map.gz emd_41469_half_map_1.map.gz emd_41469_half_map_2.map.gz | 59.9 MB 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41469 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41469 | HTTPS FTP |
-Related structure data
Related structure data | 8tp7MC 8tp2C 8tp3C 8tp4C 8tp5C 8tp6C 8tp9C 8tpaC 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_41469.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targeting Fab 4-1-1G03 | ||||||||||||||||||||
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
File | emd_41469_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Additional Map
File | emd_41469_additional_1.map | ||||||||||||
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Annotation | Additional Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_41469_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_41469_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targetin...
Entire | Name: H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targeting Fab 4-1-1G03 |
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Components |
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-Supramolecule #1: H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targetin...
Supramolecule | Name: H2 hemagglutinin (A/Singapore/1/1957) in complex with Sa-targeting Fab 4-1-1G03 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Influenza A virus (A/Singapore/1/1957(H2N2)) |
-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 (A/Singapore/1/1957(H2N2)) |
Molecular weight | Theoretical: 63.17852 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAIIYLILLF TAVRGDQICI GYHANNSTEK VDTILERNVT VTHAKDILEK THNGKLCKLN GIPPLELGDC SIAGWLLGNP ECDRLLSVP EWSYIMEKEN PRDGLCYPGS FNDYEELKHL LSSVKHFEKV KILPKDRWTQ HTTTGGSRAC AVSGNPSFFR N MVWLTKKG ...String: MAIIYLILLF TAVRGDQICI GYHANNSTEK VDTILERNVT VTHAKDILEK THNGKLCKLN GIPPLELGDC SIAGWLLGNP ECDRLLSVP EWSYIMEKEN PRDGLCYPGS FNDYEELKHL LSSVKHFEKV KILPKDRWTQ HTTTGGSRAC AVSGNPSFFR N MVWLTKKG SNYPVAKGSY NNTSGEQMLI IWGVHHPNDE TEQRTLYQNV GTYVSVGTST LNKRSTPDIA TRPKVNGQGG RM EFSWTLL DMWDTINFES TGNLIAPEYG FKISKRGSSG IMKTEGTLEN CETKCQTPLG AINTTLPFHN VHPLTIGECP KYV KSEKLV LATGLRNVPQ IESRGLFGAI AGFIEGGWQG MVDGWYGYHH SNDQGSGYAA DKESTQKAFD GITNKVNSVI EKMN TQFEA VGKEFSNLER RLENLNKKME DGFLDVWTYN AELLVLMENE RTLDFHDSNV KNLYDKVRMQ LRDNVKELGN GCFEF YHKC DDECMNSVKN GTYDYPKYEE ESKLNRNEIK GVKLSSMGVY QILAIYATVA GSLSLAIMMA GISFWMCSNG SLQCRI CI UniProtKB: Hemagglutinin |
-Macromolecule #2: Heavy chain of monoclonal antibody 4-1-1G03
Macromolecule | Name: Heavy chain of monoclonal antibody 4-1-1G03 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.907326 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKTSETLSL TCAVSGGSIS GSRYYWAWIR QPPGKGLEWI GNLYYSGTNF YNPSLEGRVT ISVDTSKNQV SLKLSSVTA ADTAVYFCAR HVYYSDTNSY TYFFDYWGQG TLVTVSS |
-Macromolecule #3: Light chain of monoclonal antibody 4-1-1G03
Macromolecule | Name: Light chain of monoclonal antibody 4-1-1G03 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.237258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ALTQPASVSG SPGQSITISC TGTSSDIGGY NYVSWYQNHP GKAPKLIIYD VSHRPSGVSN RFSGSKSGNT ASLSISGLQA EDEADYYCC SFTDNNIPAF GGGTKLTVL |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |