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- EMDB-44903: Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-44903
TitleVaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer
Map datasharpened map
Sample
  • Complex: Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: Fab c115.131 heavy chain
    • Protein or peptide: Fab c115.131 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVaccine / VIRAL PROTEIN-IMMUNE SYSTEM complex / IMMUNE SYSTEM
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 speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Simons FoundationSF349247 United States
CitationJournal: Sci Transl Med / Year: 2025
Title: Vaccination with different group 2 influenza subtypes alters epitope targeting and breadth of hemagglutinin stem-specific human B cells.
Authors: Grace E Mantus / Ankita J Chopde / Jason Gorman / Lauren Y Cominsky / Amine Ourahmane / Adrian Creanga / Geoffrey D Shimberg / Rebecca A Gillespie / David J Van Wazer / Tongqing Zhou / ...Authors: Grace E Mantus / Ankita J Chopde / Jason Gorman / Lauren Y Cominsky / Amine Ourahmane / Adrian Creanga / Geoffrey D Shimberg / Rebecca A Gillespie / David J Van Wazer / Tongqing Zhou / Suprabhath R Gajjala / Connor Williams / Emma Maestle / Douglas S Reed / Leonid Serebryannyy / Pamela Costner / Lasonji Holman / Joseph P Casazza / Richard A Koup / Lesia K Dropulic / Peter D Kwong / Adrian B McDermott / Masaru Kanekiyo / Sarah F Andrews /
Abstract: The conserved influenza hemagglutinin stem, which is a target of cross-neutralizing antibodies, is now used in vaccine strategies focused on protecting against influenza pandemics. Antibody responses ...The conserved influenza hemagglutinin stem, which is a target of cross-neutralizing antibodies, is now used in vaccine strategies focused on protecting against influenza pandemics. Antibody responses to group 1 stem have been extensively characterized, but little is known about group 2. Here, we characterized the stem-specific repertoire of individuals vaccinated with one of three group 2 influenza subtypes (H3, H7, or H10). Epitope mapping revealed two epitope supersites on the group 2 stem. Antibodies targeting the central epitope were broadly cross-reactive, whereas antibodies targeting the lower epitope had narrower breadth but higher potency against H3 subtypes. The ratio of B cells targeting each of the supersites varied with the vaccine subtype, leading to differences in the cross-reactivity of the B cell response. Our findings suggest that vaccine strategies targeting both group 2 stem epitopes would be complementary, eliciting broader and more potent protection against both seasonal and pandemic influenza strains.
History
DepositionMay 16, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44903.png

Downloads & links

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Map

FileDownload / File: emd_44903.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 344.32 Å		1.08 Å/pix.
x 320 pix.
= 344.32 Å		1.08 Å/pix.
x 320 pix.
= 344.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.7601986 - 1.5495586
Average (Standard dev.)0.0022873136 (±0.029893741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44903_msk_1.map
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Additional map: resolve map

Fileemd_44903_additional_1.map
Annotationresolve map
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Additional map: unsharpened map

Fileemd_44903_additional_2.map
Annotationunsharpened map
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Half map: half map B

Fileemd_44903_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_44903_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer

EntireName: Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer
Components
  • Complex: Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: Fab c115.131 heavy chain
    • Protein or peptide: Fab c115.131 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer

SupramoleculeName: Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 35.569184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLDKICLGHH AVANGTIVKT LTNEQEEVTN ATETVESTGI NRLCMKGRKH KDLGNCHPIG MLIGTPACDL HLTGMWDTLI ERENAIAYC YPGATVNVEA LRQKIMESGG INKISTGFTY GSSINSAGTT RACMRNGGNS FYAELKWLVS KSKGQNFPQT T NTYRNTDT ...String:
GLDKICLGHH AVANGTIVKT LTNEQEEVTN ATETVESTGI NRLCMKGRKH KDLGNCHPIG MLIGTPACDL HLTGMWDTLI ERENAIAYC YPGATVNVEA LRQKIMESGG INKISTGFTY GSSINSAGTT RACMRNGGNS FYAELKWLVS KSKGQNFPQT T NTYRNTDT AEHLIMWGIH HPSSTQEKND LYGTQSLSIS VGSSTYRNNF VPVVGARPQV NGQSGRIDFH WTLVQPGDNI TF SHNGGLI APSRVSKLIG RGLGIQSDAP IDNNCESKCF WRGGSINTRL PFQNLSPRTV GQCPKYVNRR SLMLATGMRN VPE LIQGR

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 26.338871 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFL ENGWEGMVDG WYGFRHQNAQ GTGQAADYKS TQAAIDQITG KLNRLVEKTN TEFESIESEF SEIEHQIGNV INWTKDSIT DIWTYQAELL VAMENQHTID MADSEMLNLY ERVRKQLRQN AEEDGKGCFE IYHACDDSCM ESIRNNTYDH S QYREEALL ...String:
GLFGAIAGFL ENGWEGMVDG WYGFRHQNAQ GTGQAADYKS TQAAIDQITG KLNRLVEKTN TEFESIESEF SEIEHQIGNV INWTKDSIT DIWTYQAELL VAMENQHTID MADSEMLNLY ERVRKQLRQN AEEDGKGCFE IYHACDDSCM ESIRNNTYDH S QYREEALL NRLNINPVTG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGS GLNDIFEAQK IEWHEGHHHH HH

UniProtKB: Hemagglutinin

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Macromolecule #3: Fab c115.131 heavy chain

MacromoleculeName: Fab c115.131 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.195551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGG LVQPGGSLRL SCVASGFTFS AYAMSWVRQA PGKGLEWVSS VSGGGYNTNY ADSVRGRFTA SIDNSKRTLY LQMNSLRAE DTAVYYCAKD RNWDPPYYFD SWGQGTLVTV SS

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Macromolecule #4: Fab c115.131 light chain

MacromoleculeName: Fab c115.131 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.640926 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVVMTQSPAT LSVSPGERAT LSCRASQSVS SKLAWYQQTP GQAPRLLIYG ASTRATDIPA RFSGSGSGTE FTLTISGLQS EDFAVYYCQ QYNNWPRTFG QGTKLEIK

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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: 9 / 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 / Details: PBS
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2831 / Average exposure time: 2.0 sec. / Average electron dose: 52.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98574
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9bu8:
Vaccine elicited Fab c115.131 with influenza H10 JD13 HA trimer

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