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- EMDB-44452: Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44452
TitleInfluenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647
Map datadeepEMhancer sharpened map
Sample
  • Complex: Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab ADI-85647 Heavy chain
    • Protein or peptide: Ig-like domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / Influenza A / Antibody / Fab / VIRAL PROTEIN
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 / extracellular region / membrane
Similarity search - Function
: / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Hemagglutinin / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsFerreira Ramos AS / Bajic G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Sci Adv / Year: 2025
Title: Conserved sites on the influenza H1 and H3 hemagglutinin recognized by human antibodies.
Authors: Daniel P Maurer / Mya Vu / Ana Sofia Ferreira Ramos / Haley L Dugan / Paul Khalife / James C Geoghegan / Laura M Walker / Goran Bajic / Aaron G Schmidt /
Abstract: Monoclonal antibodies (mAbs) targeting the influenza hemagglutinin (HA) can be used as prophylactics or templates for next-generation vaccines. Here, we isolated broad, subtype-neutralizing mAbs from ...Monoclonal antibodies (mAbs) targeting the influenza hemagglutinin (HA) can be used as prophylactics or templates for next-generation vaccines. Here, we isolated broad, subtype-neutralizing mAbs from human B cells recognizing the H1 or H3 HA "head" and a mAb engaging the conserved stem. The H1 mAbs bind the lateral patch epitope on HAs from 1933 to 2021 and a prepandemic swine H1N1 virus. We improved neutralization potency using directed evolution toward a contemporary H1 HA. Deep mutational scanning of four antigenically distinct H1N1 viruses identified potential viral escape pathways. For the H3 mAbs, we used cryo-electron microscopy to define their epitopes: One mAb binds the side of the HA head, accommodating the N133 glycan and a pocket underneath the receptor binding site; the other mAb recognizes an HA stem epitope that partially overlaps with previously characterized mAbs but with distinct antibody variable genes. Collectively, these mAbs identify conserved sites recognized by broadly-reactive mAbs that may be elicited by next-generation vaccines.
History
DepositionApr 11, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44452.png

Downloads & links

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Map

FileDownload / File: emd_44452.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0018332134 - 1.6860164
Average (Standard dev.)0.0013224204 (±0.026118843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_44452_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryoSPARC sharpened map

Fileemd_44452_additional_2.map
AnnotationcryoSPARC sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_44452_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_44452_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 : Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with ...

EntireName: Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647
Components
  • Complex: Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab ADI-85647 Heavy chain
    • Protein or peptide: Ig-like domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with ...

SupramoleculeName: Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 57.485398 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QKIPGNDNST ATLCLGHHAV PNGTIVKTIT NDRIEVTNAT ELVQNSSIGE ICGSPHQILD GGNCTLIDAL LGDPQCDGFQ NKEWDLFVE RSRANSNCYP YDVPDYASLR SLVASSGTLE FKNESFNWTG VKQNGTSSAC IRGSSSSFFS RLNWLTSLNN I YPAQNVTM ...String:
QKIPGNDNST ATLCLGHHAV PNGTIVKTIT NDRIEVTNAT ELVQNSSIGE ICGSPHQILD GGNCTLIDAL LGDPQCDGFQ NKEWDLFVE RSRANSNCYP YDVPDYASLR SLVASSGTLE FKNESFNWTG VKQNGTSSAC IRGSSSSFFS RLNWLTSLNN I YPAQNVTM PNKEQFDKLY IWGVHHPDTD KNQISLFAQS SGRITVSTKR SQQAVIPNIG SRPRIRDIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC KSECITPNGS IPNDKPFQNV NRITYGACPR YVKQSTLKLA TGM RNVPEK QTRGIFGAIA GFIENGWEGM VDGWYGFRWQ NSEGRGQAAD LKSTQAAIDQ INGILNRLIG KTNEKFHQIE KEFS EVEGR VQDLEKYVED TKIDLWSYNA ELLVALINQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIGS IRNE TYDHNVYRDE ALNNRFQIKG AGSSLEVLFQ

UniProtKB: Hemagglutinin

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Macromolecule #2: Fab ADI-85647 Heavy chain

MacromoleculeName: Fab ADI-85647 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.631689 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGRSLRL SCAASGFTFH NYAMHWVRQA PGKGLDWVTG ITWNSVNVDY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTALYYCVKG QVWSGYYLTH DAFDLWGQGT TVTVSGASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLVESGGG LVQPGRSLRL SCAASGFTFH NYAMHWVRQA PGKGLDWVTG ITWNSVNVDY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTALYYCVKG QVWSGYYLTH DAFDLWGQGT TVTVSGASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DKGSSLEVLF Q

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Macromolecule #3: Ig-like domain-containing protein

MacromoleculeName: Ig-like domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.241902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPPS LSATVGDRVT ITCRASQSIS NYLNWYQQKP GKAPKLLISG ASSLQLGVPS RFSGSESGTD FTLTISSLQP EDCATYYCQ QGYIMPGTFG QGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIVMTQSPPS LSATVGDRVT ITCRASQSIS NYLNWYQQKP GKAPKLLISG ASSLQLGVPS RFSGSESGTD FTLTISSLQP EDCATYYCQ QGYIMPGTFG QGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

UniProtKB: Ig-like domain-containing protein

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 7 / 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: 7.5
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Details: Solarus plasma cleaner machine (Gatan)
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 20 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.1) / Number images used: 315433
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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