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- EMDB-75901: Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmet... -

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Basic information

Entry
Database: EMDB / ID: EMD-75901
TitleInfluenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
Map dataInfluenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
Sample
  • Complex: Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
    • Protein or peptide: Hemagglutinin
KeywordsHemagglutinin / Influenza A virus / H3N2 / Viral Entry / Trimer / Glycoprotein / Membrane Fusion / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsubtomogram averaging / cryo EM / Resolution: 7.0 Å
AuthorsEnos SE / Cook BD / Rahmani H / Narehood SM / Li Y / Kuschnerus IC / Redford HT / Dukakis P / Ji D / Bachochin MJ ...Enos SE / Cook BD / Rahmani H / Narehood SM / Li Y / Kuschnerus IC / Redford HT / Dukakis P / Ji D / Bachochin MJ / Grotjahn DA / Herzik MA
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM138206 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD032471 United States
Other privateSearle Scholars United States
Other privateCottrell Scholars United States
Other privateGeorge W. and Carol A. Lattimer Faculty Research Fellowship United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM154216-02 United States
CitationJournal: bioRxiv / Year: 2026
Title: A Surfactant Cocktail Overcomes Air-Water Interface Artifacts in Single-Particle CryoEM.
Authors: Suzanne E Enos / Brian D Cook / Hamidreza Rahmani / Sarah M Narehood / Yizhou Li / Inga C Kuschnerus / Trevor H Redford / Peter Dukakis / Daniel Ji / Maxwell J Bachochin / Danielle A Grotjahn / Mark A Herzik
Abstract: Single-particle cryogenic electron microscopy (cryoEM) is a widely used technique for structure determination of biomacromolecules to near-atomic resolution. Random distributions of these molecules ...Single-particle cryogenic electron microscopy (cryoEM) is a widely used technique for structure determination of biomacromolecules to near-atomic resolution. Random distributions of these molecules in vitrified ice are necessary to accumulate enough two-dimensional views to generate a complete three-dimensional (3-D) reconstruction. However, interactions between the sample and the air-water interface (AWI) that occur during vitrification often bias the views of the sample, a phenomenon termed preferred orientation, limiting our ability to obtain 3-D reconstructions. Surfactants are often used as sample additives to prevent AWI-induced deterioration, but no general strategy exists for surfactant choice, requiring laborious screening for each sample. To circumvent these issues, we developed SurfACT, a cocktail of diverse surfactants with distinct physicochemical properties that limits AWI-dependent sample denaturation and orientation bias, while mitigating individual surfactant-specific drawbacks. Here we demonstrate SurfACT's effectiveness with four proteins plagued by AWI-induced issues, including two species of hemagglutinin (HA), molybdenum-iron protein (MoFeP) from the nitrogenase enzyme, and aldolase. All four samples show drastically improved viewing distribution and map completeness when SurfACT is applied. Cryogenic electron tomography demonstrates that SurfACT redistributes particles from the AWI into the bulk ice, driving signal recovery and inhibiting denaturation. This versatile sample additive minimizes sample-specific screening and expands the capabilities and range of suitable samples for cryoEM.
History
DepositionMar 6, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75901.png

Downloads & links

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Map

FileDownload / File: emd_75901.map.gz / Format: CCP4 / Size: 56.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfluenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.11 Å/pix.
x 246 pix.
= 519.06 Å		2.11 Å/pix.
x 246 pix.
= 519.06 Å		2.11 Å/pix.
x 246 pix.
= 519.06 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00364
Minimum - Maximum-0.0038690341 - 0.009390757
Average (Standard dev.)0.000009221508 (±0.0002639571)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions246246246
Spacing246246246
CellA=B=C: 519.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75901_msk_1.map
Projections & Slices
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Additional map: Unsharpened map of Influenza A virus Hemagglutinin (A/Darwin/6/2021...

Fileemd_75901_additional_1.map
AnnotationUnsharpened map of Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
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Half map: Half map A of Influenza A virus Hemagglutinin...

Fileemd_75901_half_map_1.map
AnnotationHalf map A of Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) determined using the SPT Labtech chameleon in the presence of 0x SurfACT; C3 symmetry; subtomogram averaged
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of Influenza A virus Hemagglutinin...

Fileemd_75901_half_map_2.map
AnnotationHalf map B of Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) determined using the SPT Labtech chameleon in the presence of 0x SurfACT; C3 symmetry; subtomogram averaged
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 (A/Darwin/6/2021 H3N2) (C3 symmet...

EntireName: Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
Components
  • Complex: Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
    • Protein or peptide: Hemagglutinin

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Supramolecule #1: Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmet...

SupramoleculeName: Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry; subtomogram averaged) determined using the SPT Labtech chameleon in the presence of 0x SurfACT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 185 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSNI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICGS PHQILDGGNC TLIDALLGDP QCDGFQNKEW DLFVERSRAN SNCYPYDVPD YASLRSLVAS SGTLEFKNES FNWTGVKQNG TSSACIRGSS SSFFSRLNWL ...String:
MKTIIALSNI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICGS PHQILDGGNC TLIDALLGDP QCDGFQNKEW DLFVERSRAN SNCYPYDVPD YASLRSLVAS SGTLEFKNES FNWTGVKQNG TSSACIRGSS SSFFSRLNWL TSLNNIYPAQ NVTMPNKEQF DKLYIWGVHH PDTDKNQISL FAQSSGRITV STKRSQQAVI PNIGSRPRIR DIPSRISIYW TIVKPGDILL INSTGNLIAP RGYFKIRSGK SSIMRSDAPI GKCKSECITP NGSIPNDKPF QNVNRITYGA CPRYVKQSTL KLATGMRNVP EKQTRGIFGA IAGFIENGWE GMVDGWYGFR HQNSEGRGQA ADLKSTQAAI DQINGKLNRL IGKTNEKFHQ IEKEFSEVEG RVQDLEKYVE DTKIDLWSYN AELLVALENQ HTIDLTDSEM NKLFEKTKKQ LRENAEDMGN GCFKIYHKCD NACIGSIRNE TYDHNVYRDE ALNNRFQIKG Vgyipeaprd gqayvrkdge wvllstflgs enlyfqggsh hhhhh

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
50.0 mMNH2C(CH2OH)3-HClTRIS
150.0 mMNaClSodium Chloride
GridModel: Quantifoil Active R1.2/0.8 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298.15 K / Instrument: SPT LABTECH CHAMELEON
Details: Samples were frozen with the SPT Labtech chameleon.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 1 / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 3.8000000000000003 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5)
Details: Duplicates were removed using a python code, no classification was performed.
Number subtomograms used: 20267
ExtractionNumber tomograms: 3 / Number images used: 25474 / Software - Name: Warp / Software - details: WarpTools
CTF correctionSoftware - Name: Warp / Software - details: WarpTools / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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