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Yorodumi- EMDB-33024: Cryo-EM structure of H1 hemagglutinin from A/Washington/05/2011 i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33024 | |||||||||
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Title | Cryo-EM structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Cong Y / Liu CX | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Unique binding pattern for a lineage of human antibodies with broad reactivity against influenza A virus. Authors: Xiaoyu Sun / Caixuan Liu / Xiao Lu / Zhiyang Ling / Chunyan Yi / Zhen Zhang / Zi Li / Mingliang Jin / Wenshuai Wang / Shubing Tang / Fangfang Wang / Fang Wang / Sonam Wangmo / Shuangfeng ...Authors: Xiaoyu Sun / Caixuan Liu / Xiao Lu / Zhiyang Ling / Chunyan Yi / Zhen Zhang / Zi Li / Mingliang Jin / Wenshuai Wang / Shubing Tang / Fangfang Wang / Fang Wang / Sonam Wangmo / Shuangfeng Chen / Li Li / Liyan Ma / Yaguang Zhang / Zhuo Yang / Xiaoping Dong / Zhikang Qian / Jianping Ding / Dayan Wang / Yao Cong / Bing Sun / Abstract: Most structurally characterized broadly neutralizing antibodies (bnAbs) against influenza A viruses (IAVs) target the conserved conformational epitopes of hemagglutinin (HA). Here, we report a ...Most structurally characterized broadly neutralizing antibodies (bnAbs) against influenza A viruses (IAVs) target the conserved conformational epitopes of hemagglutinin (HA). Here, we report a lineage of naturally occurring human antibodies sharing the same germline gene, V3-48/V1-12. These antibodies broadly neutralize the major circulating strains of IAV in vitro and in vivo mainly by binding a contiguous epitope of H3N2 HA, but a conformational epitope of H1N1 HA, respectively. Our structural and functional studies of antibody 28-12 revealed that the continuous amino acids in helix A, particularly N49 of H3 HA, are critical to determine the binding feature with 28-12. In contrast, the conformational epitope feature is dependent on the discontinuous segments involving helix A, the fusion peptide, and several HA1 residues within H1N1 HA. We report that this antibody was initially selected by H3 (group 2) viruses and evolved via somatic hypermutation to enhance the reactivity to H3 and acquire cross-neutralization to H1 (group 1) virus. These findings enrich our understanding of different antigenic determinants of heterosubtypic influenza viruses for the recognition of bnAbs and provide a reference for the design of influenza vaccines and more effective antiviral drugs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33024.map.gz | 36.2 MB | EMDB map data format | |
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Header (meta data) | emd-33024-v30.xml emd-33024.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_33024.png | 76.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33024 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33024 | HTTPS FTP |
-Validation report
Summary document | emd_33024_validation.pdf.gz | 322.2 KB | Display | EMDB validaton report |
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Full document | emd_33024_full_validation.pdf.gz | 321.8 KB | Display | |
Data in XML | emd_33024_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_33024_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33024 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33024 | HTTPS FTP |
-Related structure data
Related structure data | 7x6oMC 7x6lC 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_33024.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.318 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : H1 hemagglutinin from A/Washington/05/2011 in complex with a neut...
Entire | Name: H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12 |
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Components |
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-Supramolecule #1: H1 hemagglutinin from A/Washington/05/2011 in complex with a neut...
Supramolecule | Name: H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Influenza A virus |
Recombinant expression | Organism: Insecta environmental sample (insect) |
-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 |
Molecular weight | Theoretical: 37.055742 KDa |
Recombinant expression | Organism: Insecta environmental sample (insect) |
Sequence | String: TFATANSDTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVET SSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK GFYKNLIWLV K KGNSYPKL ...String: TFATANSDTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVET SSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK GFYKNLIWLV K KGNSYPKL SKSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADTYVFV GTSRYSKKFK PEIAIRPKVR DQEGRMNYYW TL VEPGDKI TFEATGNLVV PRYAFAMERN AGSGIIISDT PVHDCNTTCQ TPKGAINTSL PFQNIHPITI GKCPKYVKST KLR LATGLR NVPSIQSR |
-Macromolecule #2: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus / Strain: A/Freiburg/728006/2011(H1N1) |
Molecular weight | Theoretical: 20.160332 KDa |
Recombinant expression | Organism: Insecta environmental sample (insect) |
Sequence | String: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREEIDGV |
-Macromolecule #3: Heavy chain of antibody 12 fab
Macromolecule | Name: Heavy chain of antibody 12 fab / 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: 24.466277 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGFTFS TYNMNWVRQA PGKGLEWLSY ISTSSNTIYY ADSVKGRFTI SRDNAKNSLF LQMNSLRDE DTAVYYCARD RGCSSTNCYV VGYYFYGMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String: EVQLVESGGG LVQPGGSLRL SCAASGFTFS TYNMNWVRQA PGKGLEWLSY ISTSSNTIYY ADSVKGRFTI SRDNAKNSLF LQMNSLRDE DTAVYYCARD RGCSSTNCYV VGYYFYGMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV E |
-Macromolecule #4: The light chain of antibody 12 fab
Macromolecule | Name: The light chain of antibody 12 fab / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.264861 KDa |
Recombinant expression | Organism: Insecta environmental sample (insect) |
Sequence | String: DIQMTQSPSS VSASVGDRVT ITCRASQGIS SYLAWYQLKP GRAPKLLIYG ATRLQSGVPS RFSGSGSGTD FTLTISGLQP EDFATYHCQ QADSFPLTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS VSASVGDRVT ITCRASQGIS SYLAWYQLKP GRAPKLLIYG ATRLQSGVPS RFSGSGSGTD FTLTISGLQP EDFATYHCQ QADSFPLTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 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: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124947 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |