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- EMDB-41471: H1 hemagglutinin (NC99) in complex with medial-junction-targeting... -

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Basic information

Entry
Database: EMDB / ID: EMD-41471
TitleH1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
Map dataH1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
Sample
  • Complex: H1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Heavy chain of Fab 2-2-1G06
    • Protein or peptide: Light chain of Fab 2-2-1G06
    • Protein or peptide: Hemagglutinin HA2 chain
  • 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/New Caledonia/20/1999(H1N1)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: bioRxiv / Year: 2023
Title: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.
Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / 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 / Abigail M Jackson / Alesandra J Rodriguez / 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 I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in ...Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin 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.
History
DepositionAug 4, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41471.png

Downloads & links

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Map

FileDownload / File: emd_41471.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
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: 0.359
Minimum - Maximum-1.5583104 - 2.6003034
Average (Standard dev.)-0.0001931261 (±0.057651807)
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_41471_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_41471_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_41471_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_41471_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 : H1 hemagglutinin (NC99) in complex with medial-junction-targeting...

EntireName: H1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
Components
  • Complex: H1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Heavy chain of Fab 2-2-1G06
    • Protein or peptide: Light chain of Fab 2-2-1G06
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H1 hemagglutinin (NC99) in complex with medial-junction-targeting...

SupramoleculeName: H1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (A/New Caledonia/20/1999(H1N1))

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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 (A/New Caledonia/20/1999(H1N1))
Molecular weightTheoretical: 38.289207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT ...String:
MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT GKNGLYPNLS KSYVNNKEKE VLVLWGVHHP PNIGNQRALY HTENAYVSVV SSHYSRRFTP EIAKRPKVRD QE GRINYYW TLLEPGDTII FEANGNLIAP WYAFALSRGF GSGIITSNAP MDECDAKCQT PQGAINSSLP FQNVHPVTIG ECP KYVRSA KLRMVTGLRN IPSIQSR

UniProtKB: Hemagglutinin

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Macromolecule #2: Heavy chain of Fab 2-2-1G06

MacromoleculeName: Heavy chain of Fab 2-2-1G06 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.02063 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLRESGPG LVKPSQTLSL TCTVSGDSIS NGGLYWNWIR QRPGRGLEWI GYIYYNGVTT YNPSLRSRIA ISLETAKNQL SLRLSSVSA ADTAIYYCAR EGWVPDYGGR NYYLDFWGQG TLVTVSS

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Macromolecule #3: Light chain of Fab 2-2-1G06

MacromoleculeName: Light chain of Fab 2-2-1G06 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.781154 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASHNIQ NFLNWYQQKP GKAPKLLIYA ASTLQSGVPS RFSGSGSRTD FTLTISSLQP EDFAAYYCQ QSYGLPRTFG QGTRLEIK

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Macromolecule #4: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/New Caledonia/20/1999(H1N1))
Molecular weightTheoretical: 25.065277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY P KYSEESKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY P KYSEESKL NREKIDGVKL ESMGVYQILA IYSTVASSLV LLVSLGAISF WMCSNGSLQC RICI

UniProtKB: Hemagglutinin

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / 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: 48.6 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124412
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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