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- EMDB-48078: Cryo-EM structure of 5E10 Fab in complex with H3 influenza Singap... -

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Basic information

Entry
Database: EMDB / ID: EMD-48078
TitleCryo-EM structure of 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer
Map datasharpened map
Sample
  • Complex: 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHA / influenza / flu / N-term / H3 / sing16 / IMMUNE SYSTEM
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 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: Structure / Year: 2025
Title: The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody.
Authors: Reda Rawi / Nicholas C Morano / Crystal Sao-Fong Cheung / Haijuan Du / Jason Gorman / Madhu Prabhakaran / Jordan E Becker / Tatsiana Bylund / Sam Charaf / Xuejun Chen / Myungjin Lee / Darcy ...Authors: Reda Rawi / Nicholas C Morano / Crystal Sao-Fong Cheung / Haijuan Du / Jason Gorman / Madhu Prabhakaran / Jordan E Becker / Tatsiana Bylund / Sam Charaf / Xuejun Chen / Myungjin Lee / Darcy R Harris / Adam S Olia / Li Ou / Lingshu Wang / Shuishu Wang / Baoshan Zhang / Masaru Kanekiyo / Adrian B McDermott / Tongqing Zhou / Lawrence Shapiro / Peter D Kwong /
Abstract: The N terminus of the H3 subtype of influenza virus hemagglutinin is ∼10 residues longer than the N termini of most other hemagglutinins. As conserved, exposed, and linear regions may be good ...The N terminus of the H3 subtype of influenza virus hemagglutinin is ∼10 residues longer than the N termini of most other hemagglutinins. As conserved, exposed, and linear regions may be good vaccine targets, we investigated the vaccine utility of the extended H3-N terminus. First, we identified antibody 5E10, for which structure and binding analyses revealed recognition of the H3-N terminus. Second, we immunized mice with immunogens incorporating the H3-N terminus, boosted with hemagglutinin trimer, and isolated antibodies from immunogen-elicited B cells that bound both H3-N terminus and hemagglutinin trimer. However, hemagglutinin-complex structures of two such antibodies, 3864-6 and 3864-10, that neutralized H3-influenza strains, revealed only peripheral recognition of the hemagglutinin N terminus. Collectively, these results reveal the N terminus of H3 hemagglutinin to be a suboptimal vaccine target and suggest that-in addition to being conserved, flexible, and accessible-other factors influence the elicitation of potent broadly neutralizing responses.
History
DepositionNov 25, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48078.png

Downloads & links

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Map

FileDownload / File: emd_48078.map.gz / Format: CCP4 / Size: 244.1 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 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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.7592212 - 1.6179699
Average (Standard dev.)0.0010359259 (±0.041782632)
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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Mask #1

Fileemd_48078_msk_1.map
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Additional map: unsharpened map

Fileemd_48078_additional_1.map
Annotationunsharpened map
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Half map: half map A

Fileemd_48078_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_48078_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer

EntireName: 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer
Components
  • Complex: 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer

SupramoleculeName: 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: 5E10 fab not built
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: 37.357293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKIPGNDNST ATLCLGHHAV PNGTIVKTIC NDRIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FKNESFNWTG VTQNGTSSAC IRGSSSSFFS RLNWLTHLNY T YPALNVTM ...String:
QKIPGNDNST ATLCLGHHAV PNGTIVKTIC NDRIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FKNESFNWTG VTQNGTSSAC IRGSSSSFFS RLNWLTHLNY T YPALNVTM PNKEQFDKLY IWGVHHPGTD KDQIFLYAQS SGRITVSTKR SQQAVIPNIG SRPRIRDIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC KSECITPNGS IPNDKPFQNV NRITYGACPR YVKHSTLKLA TGM RNVPEK QTRRRRRR

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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: 26.630529 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDQING KLNRLIGKTN EKFHQIEKEF SEVEGRVQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI ESIRNETYDH N VYRDEALN ...String:
GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDQING KLNRLIGKTN EKFHQIEKEF SEVEGRVQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI ESIRNETYDH N VYRDEALN NRFQIKGVEG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHHASWSHP QFEK

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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: 17 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.19 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

CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 28375
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3)

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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-9ei8:
Cryo-EM structure of 5E10 Fab in complex with H3 influenza Singapore 2016 HA trimer

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