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- EMDB-43529: L5A7 Fab bound to Indonesia2005 Hemagglutinin -

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Basic information

Entry
Database: EMDB / ID: EMD-43529
TitleL5A7 Fab bound to Indonesia2005 Hemagglutinin
Map data
Sample
  • Complex: Complex of L5A7 Fab and Indonesia2005 HA
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: L5A7 Fab Heavy Chain
    • Protein or peptide: L5A7 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / 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 / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsOlia AS / Gorman J / 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 29, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43529.png

Downloads & links

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Map

FileDownload / File: emd_43529.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 433.2 Å		1.08 Å/pix.
x 400 pix.
= 433.2 Å		1.08 Å/pix.
x 400 pix.
= 433.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.71990186 - 1.2105743
Average (Standard dev.)0.0006518671 (±0.02550502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 433.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43529_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43529_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 Indonesia2005 HA

EntireName: Complex of L5A7 Fab and Indonesia2005 HA
Components
  • Complex: Complex of L5A7 Fab and Indonesia2005 HA
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: L5A7 Fab Heavy Chain
    • Protein or peptide: L5A7 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of L5A7 Fab and Indonesia2005 HA

SupramoleculeName: Complex of L5A7 Fab and Indonesia2005 HA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 36.792523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 19.640781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RRKKRGLFGA IAGFIEGGWQ GMVDGWYGYH HSNEQGSGYA ADKESTQKAI DGVTNKVNSI IDKMNTQFEA VGREFNNLER RIENLNKKM EDGFLDVWTY NAELLVLMEN ERTLDFHDSN VKNLYDKVRL QLRDNAKELG NGCFEFYHKC DNECMESIRN G TYNYPQYS E

UniProtKB: Hemagglutinin

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Macromolecule #3: L5A7 Fab Heavy Chain

MacromoleculeName: L5A7 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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: 3 / 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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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
GridModel: C-flat / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.12 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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