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- EMDB-26605: H1 Solomon Islands 2006 hemagglutinin in complex with Ab109 -

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Basic information

Entry
Database: EMDB / ID: EMD-26605
TitleH1 Solomon Islands 2006 hemagglutinin in complex with Ab109
Map dataH1 Solomon Islands 2006 in complex with ab109
Sample
  • Complex: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: ab109 Fab heavy chain, ab 109 Fab light chain
      • Protein or peptide: ab109 Fab heavy chain
      • Protein or peptide: ab109 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/Solomon Islands/3/2006(H1N1)) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsWindsor IW / Caradonna TM / Schmidt AG
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI089618 United States
CitationJournal: Cell Rep / Year: 2022
Title: An epitope-enriched immunogen expands responses to a conserved viral site.
Authors: Timothy M Caradonna / Larance Ronsard / Ashraf S Yousif / Ian W Windsor / Rachel Hecht / Thalia Bracamonte-Moreno / Anne A Roffler / Max J Maron / Daniel P Maurer / Jared Feldman / Elisa ...Authors: Timothy M Caradonna / Larance Ronsard / Ashraf S Yousif / Ian W Windsor / Rachel Hecht / Thalia Bracamonte-Moreno / Anne A Roffler / Max J Maron / Daniel P Maurer / Jared Feldman / Elisa Marchiori / Ralston M Barnes / Daniel Rohrer / Nils Lonberg / Thomas H Oguin / Gregory D Sempowski / Thomas B Kepler / Masayuki Kuraoka / Daniel Lingwood / Aaron G Schmidt /
Abstract: Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting ...Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
History
DepositionApr 7, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26605.png

Downloads & links

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Map

FileDownload / File: emd_26605.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH1 Solomon Islands 2006 in complex with ab109
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.03275566 - 0.06430363
Average (Standard dev.)-1.172824e-05 (±0.0024825619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 272.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab

EntireName: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
Components
  • Complex: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: ab109 Fab heavy chain, ab 109 Fab light chain
      • Protein or peptide: ab109 Fab heavy chain
      • Protein or peptide: ab109 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab

SupramoleculeName: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: ab109 Fab heavy chain, ab 109 Fab light chain

SupramoleculeName: ab109 Fab heavy chain, ab 109 Fab light chain / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 58.608316 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPGYLLEDT ICIGYHANNS TDTVDTVLEK NVTVTHSVNL LEDSHNGKLC LLKGIAPLQL GNCSVAGWIL GNPECELLIS RESWSYIVE KPNPENGTCY PGHFADYEEL REQLSSVSSF ERFEIFPKES SWPNHTTTGV SASCSHNGES SFYKNLLWLT G KNGLYPNL ...String:
ADPGYLLEDT ICIGYHANNS TDTVDTVLEK NVTVTHSVNL LEDSHNGKLC LLKGIAPLQL GNCSVAGWIL GNPECELLIS RESWSYIVE KPNPENGTCY PGHFADYEEL REQLSSVSSF ERFEIFPKES SWPNHTTTGV SASCSHNGES SFYKNLLWLT G KNGLYPNL SKSYANNKEK EVLVLWGVHH PPNIGDQRAL YHTENAYVSV VSSHYSRKFT PEIAKRPKVR DQEGRINYYW TL LEPGDTI IFEANGNLIA PRYAFALSRG FGSGIINSNA PMDECDAKCQ TPQGAINSSL PFQNVHPVTI GECPKYVRSA KLR MVTGLR NIPSIQSRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADQKSTQ NAINGITNKV NSVIEKMNTQ FTAV GKEFN KLERRMENLN KKVDDGFIDI WTYNAELLVL LENERTLDFH DSNVKNLYEK VKSQLKNNAK EIGNGCFEFY HKCND ECME SVKNGTYDYP KYSEESKLNR EKIDGVRSGS GGALEVLFQ

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Macromolecule #2: ab109 Fab heavy chain

MacromoleculeName: ab109 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.267232 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYIHWVRQA PGQGLEWMGW INPNTGGTVY AQTFQARVTM TRDTSISTAY MELIRLRSD DTAVYYCARE RGTGAPDAFN IWGQGTLVTV SGASTKGPSV FPLAPSGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYIHWVRQA PGQGLEWMGW INPNTGGTVY AQTFQARVTM TRDTSISTAY MELIRLRSD DTAVYYCARE RGTGAPDAFN IWGQGTLVTV SGASTKGPSV FPLAPSGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC

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Macromolecule #3: ab109 Fab light chain

MacromoleculeName: ab109 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.806414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPAS LAVSLGQRAT ISCRASKSVS TSGYSYIHWY QQKPGQPPKL LIYLATNLES GVPARFSGSG SGTDFTLNIH PVEEEDAAT YYCQHSRDTP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String:
DIVMTQSPAS LAVSLGQRAT ISCRASKSVS TSGYSYIHWY QQKPGQPPKL LIYLATNLES GVPARFSGSG SGTDFTLNIH PVEEEDAAT YYCQHSRDTP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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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: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.07 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 67533
FSC plot (resolution estimation)

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