+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43529 | |||||||||
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Title | L5A7 Fab bound to Indonesia2005 Hemagglutinin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | influenza / hemagglutinin / antibody / VIRAL PROTEIN | |||||||||
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 | Homo sapiens (human) / Influenza A virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
Authors | Olia AS / Gorman J / Kwong PD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Front Immunol / Year: 2024 Title: Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody. Authors: Adam S Olia / Madhu Prabhakaran / Darcy R Harris / Crystal Sao-Fong Cheung / Rebecca A Gillespie / Jason Gorman / Abigayle Hoover / Nicholas C Morano / Amine Ourahmane / Abhinaya Srikanth / ...Authors: Adam S Olia / Madhu Prabhakaran / Darcy R Harris / Crystal Sao-Fong Cheung / Rebecca A Gillespie / Jason Gorman / Abigayle Hoover / Nicholas C Morano / Amine Ourahmane / Abhinaya Srikanth / Shuishu Wang / Weiwei Wu / Tongqing Zhou / Sarah F Andrews / Masaru Kanekiyo / Lawrence Shapiro / Adrian B McDermott / Peter D Kwong / Abstract: The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline ...The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline versions of VH6-1 antibodies, use these to sort human leukocytes, and isolate a new VH6-1-class member, antibody L5A7, which potently neutralized diverse group 1 and group 2 influenza A strains. While its heavy chain derived from the canonical IGHV6-1 heavy chain gene used by the class, L5A7 utilized a light chain gene, IGKV1-9, which had not been previously observed in other VH6-1-class antibodies. The cryo-EM structure of L5A7 in complex with Indonesia 2005 hemagglutinin revealed a nearly identical binding mode to other VH6-1-class members. The structure of L5A7 bound to the isolating anti-idiotype antibody, 28H6E11, revealed a shared surface for binding anti-idiotype and hemagglutinin that included two critical L5A7 regions: an FG motif in the third heavy chain-complementary determining region (CDR H3) and the CDR L1 loop. Surprisingly, the chemistries of L5A7 interactions with hemagglutinin and with anti-idiotype were substantially different. Overall, we demonstrate anti-idiotype-based isolation of a broad and potent influenza A virus-neutralizing antibody, revealing that anti-idiotypic selection of antibodies can involve features other than chemical mimicry of the target antigen. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43529.map.gz | 230.4 MB | EMDB map data format | |
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Header (meta data) | emd-43529-v30.xml emd-43529.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_43529.png | 44.8 KB | ||
Filedesc metadata | emd-43529.cif.gz | 6.1 KB | ||
Others | emd_43529_half_map_1.map.gz emd_43529_half_map_2.map.gz | 226.4 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43529 | HTTPS FTP |
-Validation report
Summary document | emd_43529_validation.pdf.gz | 992 KB | Display | EMDB validaton report |
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Full document | emd_43529_full_validation.pdf.gz | 991.6 KB | Display | |
Data in XML | emd_43529_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_43529_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43529 | HTTPS FTP |
-Related structure data
Related structure data | 8vueMC 8vuzC 8vvbC 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_43529.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: 1.083 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43529_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43529_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of L5A7 Fab and Indonesia2005 HA
Entire | Name: Complex of L5A7 Fab and Indonesia2005 HA |
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Components |
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-Supramolecule #1: Complex of L5A7 Fab and Indonesia2005 HA
Supramolecule | Name: Complex of L5A7 Fab and Indonesia2005 HA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: Influenza A virus |
Molecular weight | Theoretical: 36.792523 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QDQICIGYHA NNSTEQVDTI MEKNVTVTHA QDILEKTHNG KLCDLDGVKP LILRDCSVAG WLLGNPMCDE FINVPEWSYI VEKANPTND LCYPGSFNDY EELKHLLSRI NHFEKIQIIP KSSWSDHEAS SGVSSACPYL GSPSFFRNVV WLIKKNSTYP T IKKSYNNT ...String: QDQICIGYHA NNSTEQVDTI MEKNVTVTHA QDILEKTHNG KLCDLDGVKP LILRDCSVAG WLLGNPMCDE FINVPEWSYI VEKANPTND LCYPGSFNDY EELKHLLSRI NHFEKIQIIP KSSWSDHEAS SGVSSACPYL GSPSFFRNVV WLIKKNSTYP T IKKSYNNT NQEDLLVLWG IHHPNDAAEQ TRLYQNPTTY ISIGTSTLNQ RLVPKIATRS KVNGQSGRME FFWTILKPND AI NFESNGN FIAPEYAYKI VKKGDSAIMK SELEYGNCNT KCQTPMGAIN SSMPFHNIHP LTIGECPKYV KSNRLVLATG LRN SPQRES 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: Influenza A virus |
Molecular weight | Theoretical: 19.640781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RRKKRGLFGA IAGFIEGGWQ GMVDGWYGYH HSNEQGSGYA ADKESTQKAI DGVTNKVNSI IDKMNTQFEA VGREFNNLER RIENLNKKM EDGFLDVWTY NAELLVLMEN ERTLDFHDSN VKNLYDKVRL QLRDNAKELG NGCFEFYHKC DNECMESIRN G TYNYPQYS E UniProtKB: Hemagglutinin |
-Macromolecule #3: L5A7 Fab Heavy Chain
Macromolecule | Name: L5A7 Fab Heavy Chain / 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: 24.642494 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQQSGPG LVKPSQTLSL TCGISGDSVS SDAAAWDWIR QSPSRGLEWL GRTFYRSRWH HDYSESVKNR ITINADTSKN QFSLQLTSV TPEDTATYYC ARAGVRVFGI IVNSLDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String: QVQLQQSGPG LVKPSQTLSL TCGISGDSVS SDAAAWDWIR QSPSRGLEWL GRTFYRSRWH HDYSESVKNR ITINADTSKN QFSLQLTSV TPEDTATYYC ARAGVRVFGI IVNSLDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC |
-Macromolecule #4: L5A7 Fab Light Chain
Macromolecule | Name: L5A7 Fab Light Chain / 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: 22.716301 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AIQLTQSPSS LSASVGDRVT ITCRASQATS SYLAWYQQKP GKAPKLLIYA ASTLQSGVPS RFSGSGSGTD FTLTITSLQP EDFATYYCQ LSKTFGPGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST ...String: AIQLTQSPSS LSASVGDRVT ITCRASQATS SYLAWYQQKP GKAPKLLIYA ASTLQSGVPS RFSGSGSGTD FTLTITSLQP EDFATYYCQ LSKTFGPGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC |
-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: 3 / 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
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: C-flat / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.12 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: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20728 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |