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- EMDB-48079: Cryo-EM structure of 5E10 Fab in complex with H3 influenza Victor... -

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Basic information

Entry
Database: EMDB / ID: EMD-48079
TitleCryo-EM structure of 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
Map dataSharpened map
Sample
  • Complex: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
    • Protein or peptide: 5E10 Fab Heavy chain
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: 5E10 Fab Light chain
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHA / influenza / flu / N-term / H3 / 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
Biological speciesInfluenza A virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 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) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48079.png

Downloads & links

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Map

FileDownload / File: emd_48079.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.)
1.07 Å/pix.
x 400 pix.
= 429.32 Å		1.07 Å/pix.
x 400 pix.
= 429.32 Å		1.07 Å/pix.
x 400 pix.
= 429.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0733 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.4103057 - 1.7865049
Average (Standard dev.)0.0019062381 (±0.04981953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48079_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48079_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48079_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer

EntireName: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
Components
  • Complex: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
    • Protein or peptide: 5E10 Fab Heavy chain
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: 5E10 Fab Light chain
    • 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 Victoria 2011 HA trimer

SupramoleculeName: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1, #4, #2
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: 37.546414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKLPGNDNST ATLCLGHHAV PNGTIVKTIC NDQIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSNNSFFS RLNWLTQLNF K YPALNVTM ...String:
QKLPGNDNST ATLCLGHHAV PNGTIVKTIC NDQIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSNNSFFS RLNWLTQLNF K YPALNVTM PNNEQFDKLY IWGVHHPVTD KDQIFLYAQS SGRITVSTKR SQQAVIPNIG YRPRIRNIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC NSECITPNGS IPNDKPFQNV NRITYGACPR YVKQSTLKLA TGM RNVPEK QTRRRRRR

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: 25.234092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDCING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN ...String:
GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDCING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN NRFQIKGVSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: 5E10 Fab Heavy chain

MacromoleculeName: 5E10 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.463039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPG ILQPSQTLSL TCSFSGFSLS TFGMGVGWIR QPSGKGLEWL AHIWWDNDEY CNPALKSRLT ISKDTSKNHI FLKIANVDT ADTATYYCAR IFANYGGDAM DYWGQGTSVT VSSA

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Macromolecule #4: 5E10 Fab Light chain

MacromoleculeName: 5E10 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.615999 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QAVVTQESAL TTSPGGTVIL TCRSSTGAVT TSNYANWVQK KPDHLFTGLI GGTSNRVSGV PVRFSGSLIG DKAALTITGA QTEDDAMYF CALWFSTHYV FGGGTKVTVL SQ

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 20 / 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 70.51 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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 28277
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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-9ei9:
Cryo-EM structure of 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer

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