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- EMDB-55743: Cryo-EM structure of Heyndrickxia coagulans beta-galactosidase -

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Basic information

Entry
Database: EMDB / ID: EMD-55743
TitleCryo-EM structure of Heyndrickxia coagulans beta-galactosidase
Map dataSharpened map
Sample
  • Complex: beta-galactosidase hexamer
    • Protein or peptide: Beta-galactosidase LacZ
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordsbeta-galactosidase / Heyndrickxia coagulans / transgalactosylation / HYDROLASE
Function / homology
Function and homology information


galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / metal ion binding
Similarity search - Function
Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase-like / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-galactosidase LacZ
Similarity search - Component
Biological speciesHeyndrickxia coagulans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsSanita G / Maresca E / Aulitto M / Capaldi S / Esposito E / Contursi P
Funding supportEuropean Union, Italy, 4 items
OrganizationGrant numberCountry
European Union (EU)CIR01_00023European Union
European Union (EU)E63C22002170007European Union
Italian Ministry of EducationE53D23003010006 Italy
European Union (EU)CN_00000033European Union
CitationJournal: Int J Biol Macromol / Year: 2026
Title: CryoEM structural analysis of a thermophilic galactooligosaccharides-producer β-galactosidase unravels an uncommon oligomeric structure.
Authors: Gennaro Sanità / Emanuela Maresca / Stefano Capaldi / Angela Casillo / Martina Aulitto / Federica Donadio / Tillmann Pape / Maria Michela Corsaro / Emanuela Esposito / Patrizia Contursi /
Abstract: Thermostable β-galactosidases represent promising biocatalysts for lactose hydrolysis and production of structurally defined galacto-oligosaccharides (GOS). Here we report the cryo-EM structure of ...Thermostable β-galactosidases represent promising biocatalysts for lactose hydrolysis and production of structurally defined galacto-oligosaccharides (GOS). Here we report the cryo-EM structure of the glycoside hydrolase family 42 (GH42) β-galactosidase from Heyndrickxia coagulans MA-13 (HcGalB), determined at 2.97 Å resolution. HcGalB adopts a canonical tripartite architecture and assembles into a barrel-like homo-hexamer composed of two staggered trimers that interact in an unusual top-to-top configuration. This quaternary arrangement contributes not only to structural stability but also to the modulation of substrate channeling and catalytic properties. Molecular docking revealed a surface groove shaped by conserved aromatic residues that might guide the substrate towards the catalytic pocket. Moreover, the structural data provide a mechanistic rationale for the efficient transgalactosylation activity of HcGalB, which predominantly generates β (1 → 3)-linked GOS, along with β(1 → 6) and β(1 → 4) linkages, as confirmed by 2D Nuclear Magnetic Resonance. Overall, these findings expand the structural landscape of GH42 enzymes and identify architecture-specific determinants that can be leveraged to optimize GH42 catalysts for industrial and functional food applications.
History
DepositionNov 18, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55743.png

Downloads & links

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Map

FileDownload / File: emd_55743.map.gz / Format: CCP4 / Size: 216 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.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.0927898 - 1.3557652
Average (Standard dev.)0.000103704966 (±0.032198157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55743_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_55743_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55743_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_55743_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 : beta-galactosidase hexamer

EntireName: beta-galactosidase hexamer
Components
  • Complex: beta-galactosidase hexamer
    • Protein or peptide: Beta-galactosidase LacZ
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: beta-galactosidase hexamer

SupramoleculeName: beta-galactosidase hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Heyndrickxia coagulans (bacteria)

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Macromolecule #1: Beta-galactosidase LacZ

MacromoleculeName: Beta-galactosidase LacZ / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: beta-galactosidase
Source (natural)Organism: Heyndrickxia coagulans (bacteria)
Molecular weightTheoretical: 76.938195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLKKHEKFYY GGDYNPEQWD ESVWKEDMRL MKKAGVNYVS INIFSWARLQ PDEETYDFST LDKIMDMLAE NGIGVDLATA TAAPPAWLS RKYPDSLPVD KDGSRFLPGS RQHYCPNSKD YARLAAKLVR KIAERYKSHP ALVMWHVNNE YGCHISECYC D NCKKGFQT ...String:
MLKKHEKFYY GGDYNPEQWD ESVWKEDMRL MKKAGVNYVS INIFSWARLQ PDEETYDFST LDKIMDMLAE NGIGVDLATA TAAPPAWLS RKYPDSLPVD KDGSRFLPGS RQHYCPNSKD YARLAAKLVR KIAERYKSHP ALVMWHVNNE YGCHISECYC D NCKKGFQT WLKEKYGTIE NLNKSWSTDF WSQRYYEWEE ICLPGKTPTF ANPMQQLDYK AFMDDSLLAL YKMERDILKA YT PDVPVMT NLMGLHKPVD GFHWAKEMDL VTWDAYPDPF EDIPYAQFMA HDLTRSLKKQ PFLLMEQAAG AVNWRAQNAV KAP GVMRLW SYEAAAHGAD GIMFFQWRAS QGGAEKFHSG MVPHSGDEES RNFREVVQLG NELKNLEKVT GSAYASDVAI VFDW KNWWA LELDSKPSSL VTYIKQLLPF YRVLHTQNIG VDFIHPDEAM DRYKVVFAPA SYRVTKTFAD KVKAYVENGG YFATN FFSG IADENERVYL GGYPGAYRDI LGIYVEEFAP MKKGAVHQIR TGYGDAAIRV WEEKIHLKGA EALAWFKDGY LAGSPA VTA HHCGKGKAYY IGTQPDEQYL SSLLKEILKE ADVRPALDAP RGVEVAVRKN GHEKFLFLLN HTDQVQFVDA GGTYPEL IY GRTEAETVRL SPRDVKILQV IEKHHHHHH

UniProtKB: Beta-galactosidase LacZ

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 438 / 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

Concentration1.5 mg/mL
BufferpH: 5 / Component - Concentration: 100.0 mM / Component - Formula: Na3(C3H5O(COO)3) / Component - Name: sodium citrate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
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: 2794 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 799865
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 629632
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3tty


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.10.1)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ta3:
Cryo-EM structure of Heyndrickxia coagulans beta-galactosidase

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