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- EMDB-41464: H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeti... -

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Basic information

Entry
Database: EMDB / ID: EMD-41464
TitleH2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting 1-1-1F05
Map dataH2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting 1-1-1F05
Sample
  • Complex: H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting Fab 1-1-1F05
    • Protein or peptide: Heavy chain of Fab 1-1-1F05
    • Protein or peptide: Light chain of Fab 1-1-1F05
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / hemagglutinin / monoclonal antibody / immune complex / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
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/Singapore/1/1957(H2N2)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYang YR / Han J / Perrett HR / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2 T32 AI007244-36 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31Al172358 United States
CitationJournal: Cell Rep / Year: 2024
Title: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.
Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Alesandra J Rodriguez / Abigail M Jackson / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita ...Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Alesandra J Rodriguez / Abigail M Jackson / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita Chopde / Masaru Kanekiyo / Katherine V Houser / Grace L Chen / Adrian B McDermott / Sarah F Andrews / Andrew B Ward /
Abstract: Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 ...Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us to perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited. We temporally map the epitopes targeted by serum antibodies after vaccine prime and boost, revealing that previous H2 exposure results in higher responses to the variable HA head domain. In contrast, initial responses in H2-naive participants are dominated by antibodies targeting conserved epitopes. We use cryoelectron microscopy and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the HA head, including the receptor-binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses post-vaccination.
History
DepositionAug 4, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41464.png

Downloads & links

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Map

FileDownload / File: emd_41464.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting 1-1-1F05
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0177
Minimum - Maximum-0.05249427 - 0.09735027
Average (Standard dev.)0.0000021686196 (±0.0021777772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41464_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half Map-1

Fileemd_41464_half_map_1.map
Annotationhalf Map-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half Map-2

Fileemd_41464_half_map_2.map
Annotationhalf Map-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeti...

EntireName: H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting Fab 1-1-1F05
Components
  • Complex: H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting Fab 1-1-1F05
    • Protein or peptide: Heavy chain of Fab 1-1-1F05
    • Protein or peptide: Light chain of Fab 1-1-1F05
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeti...

SupramoleculeName: H2 hemagglutinin (A/Singapore/1/1957) in complex with RBS-targeting Fab 1-1-1F05
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/Singapore/1/1957(H2N2))

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Macromolecule #1: Heavy chain of Fab 1-1-1F05

MacromoleculeName: Heavy chain of Fab 1-1-1F05 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.57907 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSATLSL TCTLSGGSLS THYWSWIRQP PGKGLEYIGN IHYSGSTNYN PSLRSRVTIS VGTSKNQFSL KLTSVTAAD TAVYYCARDA PYSDFLSGVE TGWFDPWGQG TLVIVSS

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Macromolecule #2: Light chain of Fab 1-1-1F05

MacromoleculeName: Light chain of Fab 1-1-1F05 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.564807 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSVSPGERAT LSCRASQSVS SNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTD FTLTISSLQS EDFAVYSCQ QYNNWPWTFG QGTKVEIK

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.135223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAIIYLILLF TAVRGDQICI GYHANNSTEK VDTILERNVT VTHAKDILEK THNGKLCKLN GIPPLELGDC SIAGWLLGNP ECDRLLSVP EWSYIMEKEN PRDGLCYPGS FNDYEELKHL LSSVKHFEKV KILPKDRWTQ HTTTGGSRAC AVSGNPSFFR N MVWLTKKG ...String:
MAIIYLILLF TAVRGDQICI GYHANNSTEK VDTILERNVT VTHAKDILEK THNGKLCKLN GIPPLELGDC SIAGWLLGNP ECDRLLSVP EWSYIMEKEN PRDGLCYPGS FNDYEELKHL LSSVKHFEKV KILPKDRWTQ HTTTGGSRAC AVSGNPSFFR N MVWLTKKG SNYPVAKGSY NNTSGEQMLI IWGVHHPNDE TEQRTLYQNV GTYVSVGTST LNKRSTPDIA TRPKVNGQGG RM EFSWTLL DMWDTINFES TGNLIAPEYG FKISKRGSSG IMKTEGTLEN CETKCQTPLG AINTTLPFHN VHPLTIGECP KYV KSEKLV LATGLRNVPQ IESRGLFGAI AGFIEGGWQG MVDGWYGYHH SNDQGSGYAA DKESTQKAFD GITNKVNSVI EKMN TQFEA VGKEFSNLER RLENLNKKME DGFLDVWTYN AELLVLMENE RTLDFHDSNV KNLYDKVRMQ LRDNVKELGN GCFEF YHKC DDECMNSVKN GTYDYPKYEE ES

UniProtKB: Hemagglutinin

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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: 10 / 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.5 e/Å2
Electron beamAcceleration voltage: 200 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: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2wr7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 230649
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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