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- EMDB-43545: L5A7 Fab bound to 28H6E11 anti-idiotype Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-43545
TitleL5A7 Fab bound to 28H6E11 anti-idiotype Fab
Map data
Sample
  • Complex: Complex of L5A7 Fab and 28H6E11 Fab
    • Protein or peptide: L5A7 Fab Heavy Chain
    • Protein or peptide: L5A7 Fab Light Chain
  • Protein or peptide: 28H6E11 Fab Heavy Chain
  • Protein or peptide: 28H6E11 Fab Light Chain
Keywordsinfluenza / antibody / anti-idiotype / ANTIVIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsOlia AS / Morano NC / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: 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
DepositionJan 30, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43545.png

Downloads & links

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Map

FileDownload / File: emd_43545.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.73293626 - 1.0265173
Average (Standard dev.)0.00045205728 (±0.02424003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43545_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43545_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of L5A7 Fab and 28H6E11 Fab

EntireName: Complex of L5A7 Fab and 28H6E11 Fab
Components
  • Complex: Complex of L5A7 Fab and 28H6E11 Fab
    • Protein or peptide: L5A7 Fab Heavy Chain
    • Protein or peptide: L5A7 Fab Light Chain
  • Protein or peptide: 28H6E11 Fab Heavy Chain
  • Protein or peptide: 28H6E11 Fab Light Chain

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Supramolecule #1: Complex of L5A7 Fab and 28H6E11 Fab

SupramoleculeName: Complex of L5A7 Fab and 28H6E11 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 28H6E11 Fab Heavy Chain

MacromoleculeName: 28H6E11 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.499348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGPE VVRPGVSVKI SCKGSGYTFT DHAMHWVKQS HAKSLEWIGV FNTYNGDTNY NQKFEDKATM TIDKSSSTAY LELARLTSE DSAIYYCVRL GLLGFYALDY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS ...String:
QVQLQQSGPE VVRPGVSVKI SCKGSGYTFT DHAMHWVKQS HAKSLEWIGV FNTYNGDTNY NQKFEDKATM TIDKSSSTAY LELARLTSE DSAIYYCVRL GLLGFYALDY WGQGTSVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSPRPSE TVTCNVAHPA SSTKVDKKIV

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Macromolecule #2: 28H6E11 Fab Light Chain

MacromoleculeName: 28H6E11 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.146812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVLMTQTPLS LPVSLGDQAS ISCRSSQSIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DVLMTQTPLS LPVSLGDQAS ISCRSSQSIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE C

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Macromolecule #3: L5A7 Fab Heavy Chain

MacromoleculeName: L5A7 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.642494 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: L5A7 Fab Light Chain

MacromoleculeName: L5A7 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.716301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215254
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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