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- EMDB-75869: Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Lab... -

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Basic information

Entry
Database: EMDB / ID: EMD-75869
TitleRabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
Map dataRabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
Sample
  • Complex: Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
    • Protein or peptide: Fructose-bisphosphate aldolase A
  • Ligand: water
KeywordsLyase / Glycolysis / Fructose-bisphosphate aldolase / Carbon-carbon lyase
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / glycolytic process / protein homotetramerization / positive regulation of cell migration
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 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, 5 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
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 5, 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_75869.png

Downloads & links

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Map

FileDownload / File: emd_75869.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 384 pix.
= 282.24 Å		0.74 Å/pix.
x 384 pix.
= 282.24 Å		0.74 Å/pix.
x 384 pix.
= 282.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.735 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0627
Minimum - Maximum-0.21676151 - 0.33188602
Average (Standard dev.)0.00012016939 (±0.009146771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 282.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75869_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of Rabbit muscle Aldolase (D2 symmetry)...

Fileemd_75869_additional_1.map
AnnotationUnsharpened map of Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Phenix RESOLVE modified EM map of Rabbit muscle...

Fileemd_75869_additional_2.map
AnnotationPhenix RESOLVE modified EM map of Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of Rabbit muscle Aldolase determined...

Fileemd_75869_half_map_1.map
AnnotationHalf map B of Rabbit muscle Aldolase determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT; D2 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of Rabbit muscle Aldolase determined...

Fileemd_75869_half_map_2.map
AnnotationHalf map A of Rabbit muscle Aldolase determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT; D2 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Lab...

EntireName: Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
Components
  • Complex: Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
    • Protein or peptide: Fructose-bisphosphate aldolase A
  • Ligand: water

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Supramolecule #1: Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Lab...

SupramoleculeName: Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Fructose-bisphosphate aldolase A

MacromoleculeName: Fructose-bisphosphate aldolase A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 37.302602 KDa
SequenceString: HSHPALTPEQ KKELSDIAHR IVAPGKGILA ADESTGSIAK RLQSIGTENT EENRRFYRQL LLTADDRVNP CIGGVILFHE TLYQKADDG RPFPQVIKSK GGVVGIKVDK GVVPLAGTNG ETTTQGLDGL SERCAQYKKD GADFAKWRCV LKIGEHTPSA L AIMENANV ...String:
HSHPALTPEQ KKELSDIAHR IVAPGKGILA ADESTGSIAK RLQSIGTENT EENRRFYRQL LLTADDRVNP CIGGVILFHE TLYQKADDG RPFPQVIKSK GGVVGIKVDK GVVPLAGTNG ETTTQGLDGL SERCAQYKKD GADFAKWRCV LKIGEHTPSA L AIMENANV LARYASICQQ NGIVPIVEPE ILPDGDHDLK RCQYVTEKVL AAVYKALSDH HIYLEGTLLK PNMVTPGHAC TQ KYSHEEI AMATVTALRR TVPPAVTGVT FLSGGQSEEE ASINLNAINK CPLLKPWALT FSYGRALQAS ALKAWGGKKE NLK AAQEEY VKRALANSLA CQGKYTP

UniProtKB: Fructose-bisphosphate aldolase A

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1594 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium Chloride
0.05 %w/vC32H58N2O8SCHAPSO
0.0048 %w/vC20H25F13O11FOM
0.25 %w/v(C6.2H10.3O1.35N0.65Na0.35)72Amphipol A8-35
0.06 %w/v(C2H4O)nC12H26OBrij-35
GridModel: Quantifoil Active R1.2/0.8 / Material: COPPER / Support film - Material: GOLD / 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 X / 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 grids imaged: 1 / Number real images: 755 / Average exposure time: 5.0 sec. / Average electron dose: 65.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
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

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 33672
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6v20


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 51.1
Output model

PDB-11nr:
Rabbit muscle Aldolase (D2 symmetry) determined using the SPT Labtech chameleon (gold-coated grids) in the presence of 1x SurfACT

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