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- EMDB-52274: Soft-landed beta-galactosidase -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52274
TitleSoft-landed beta-galactosidase
Map dataMap of soft-landed beta-galactosidase
Sample
  • Complex: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase
Keywordsglycoside hydrolase / HYDROLASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / Resolution: 5.9 Å
AuthorsBarrass SV / Esser TK / Mowry NJ / Eriksson L / Hruby J / Seeley LT / Drabbels M / Baker LA / Rauschenbach S / Lorenz UJ
Funding support Switzerland, United Kingdom, European Union, 6 items
OrganizationGrant numberCountry
Swiss National Science Foundation213773 Switzerland
Swiss National Science Foundation207842 Switzerland
UK Research and Innovation (UKRI)EP/V051474/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V019694/1 United Kingdom
H2020 Marie Curie Actions of the European Commission883387European Union
Wellcome Trust218482/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM Sample Preparation Using Soft-landing Electrospray Ion Beam Deposition and Laser Flash Melting
Authors: Barrass SV / Esser TK / Mowry NJ / Eriksson L / Hruby J / Seeley LT / Drabbels M / Baker LA / Rauschenbach S / Lorenz UJ
History
DepositionDec 5, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52274.png

Downloads & links

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Map

FileDownload / File: emd_52274.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of soft-landed beta-galactosidase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 540 pix.
= 500.04 Å		0.93 Å/pix.
x 540 pix.
= 500.04 Å		0.93 Å/pix.
x 540 pix.
= 500.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.231
Minimum - Maximum-0.08415212 - 0.3786958
Average (Standard dev.)-0.00016307278 (±0.018990735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 500.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Locally filtered map of soft-landed beta-galactosidase

Fileemd_52274_additional_1.map
AnnotationLocally filtered map of soft-landed beta-galactosidase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of soft-landed beta-galactosidase

Fileemd_52274_half_map_1.map
AnnotationHalf map A of soft-landed beta-galactosidase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of soft-landed beta-galactosidase

Fileemd_52274_half_map_2.map
AnnotationHalf map B of soft-landed beta-galactosidase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Beta-galactosidase

EntireName: Beta-galactosidase
Components
  • Complex: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase

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Supramolecule #1: Beta-galactosidase

SupramoleculeName: Beta-galactosidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Beta-galactosidase

MacromoleculeName: Beta-galactosidase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MITDSLAVVL QRRDWENPGV TQLNRLAAHP PFASWRNSEE ARTDRPSQQL RSLNGEWRFA WFPAPEAVPE SWLECDLPEA DTVVVPSNW QMHGYDAPIY TNVTYPITVN PPFVPTENPT GCYSLTFNVD ESWLQEGQTR IIFDGVNSAF HLWCNGRWVG Y GQDSRLPS ...String:
MITDSLAVVL QRRDWENPGV TQLNRLAAHP PFASWRNSEE ARTDRPSQQL RSLNGEWRFA WFPAPEAVPE SWLECDLPEA DTVVVPSNW QMHGYDAPIY TNVTYPITVN PPFVPTENPT GCYSLTFNVD ESWLQEGQTR IIFDGVNSAF HLWCNGRWVG Y GQDSRLPS EFDLSAFLRA GENRLAVMVL RWSDGSYLED QDMWRMSGIF RDVSLLHKPT TQISDFHVAT RFNDDFSRAV LE AEVQMCG ELRDYLRVTV SLWQGETQVA SGTAPFGGEI IDERGGYADR VTLRLNVENP KLWSAEIPNL YRAVVELHTA DGT LIEAEA CDVGFRVVRI ENGLLLLNGK PLLIRGVNRH EHHPLHGQVM DEQTMVQDIL LMKQNNFNAV RCSHYPNHPL WYTL

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
DetailsBeta-galactosidase was deposited onto a cryo-EM grid using soft-landing electrospray ion beam deposition

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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) / Number grids imaged: 1 / Number real images: 945 / Average electron dose: 60.0 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 104418
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Software - details: Non-uniform refinement / Number images used: 65983
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Software - details: ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD

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