[English] 日本語
Yorodumi
- PDB-9ta3: Cryo-EM structure of Heyndrickxia coagulans beta-galactosidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ta3
TitleCryo-EM structure of Heyndrickxia coagulans beta-galactosidase
ComponentsBeta-galactosidase LacZ
KeywordsHYDROLASE / beta-galactosidase / Heyndrickxia coagulans / transgalactosylation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsSanita, G. / Maresca, E. / Aulitto, M. / Capaldi, S. / Esposito, E. / Contursi, P.
Funding supportEuropean Union, Italy, 4items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 1.1May 6, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / Item: _citation.journal_volume / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-galactosidase LacZ
B: Beta-galactosidase LacZ
C: Beta-galactosidase LacZ
D: Beta-galactosidase LacZ
E: Beta-galactosidase LacZ
F: Beta-galactosidase LacZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,23418
Polymers461,6296
Non-polymers60512
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "D"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "F"
d_5ens_1chain "E"
d_6ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISILEILEDD5 - 6635 - 663
d_12ZNZNZNZNDM700
d_21HISHISILEILEBB5 - 6635 - 663
d_22ZNZNZNZNBI700
d_31HISHISILEILECC5 - 6635 - 663
d_32ZNZNZNZNCK700
d_41HISHISILEILEFF5 - 6635 - 663
d_42ZNZNZNZNFQ700
d_51HISHISILEILEEE5 - 6635 - 663
d_52ZNZNZNZNEO700
d_61HISHISILEILEAA5 - 6635 - 663
d_62ZNZNZNZNAG700

NCS oper:
IDCodeMatrixVector
1given(0.500054894021, -0.865993707124, -4.67727426373E-5), (-0.865993707867, -0.500054894863, 7.63846040381E-6), (-3.00037975437E-5, 3.66852513159E-5, -0.999999998877)225.55201969, 390.687387438, 330.23822704
2given(0.499997827679, 0.866026657694, 2.18993107179E-5), (0.866026657967, -0.499997827438, -1.57563194719E-5), (-2.69578490849E-6, 2.68435123809E-5, -0.999999999636)-60.4374015976, 104.685379067, 330.235871705
3given(-0.499943760124, -0.866057866645, -9.12944940921E-5), (0.86605787056, -0.499943761628, -7.17046858103E-6), (-3.94320720702E-5, -8.26511461715E-5, 0.999999995807)390.696640321, 104.670956429, 0.0224390724365
4given(-0.50005008167, 0.865996446698, 0.000264818188603), (-0.86599648555, -0.500050076151, -9.14147814361E-5), (5.32574794776E-5, -0.000275043589563, 0.999999960757)104.650640723, 390.699432151, 0.0456481388936
5given(-0.999999979086, -0.000115730511351, -0.00016862482607), (-0.000115749299313, 0.999999987095, 0.000111413218903), (0.000168611929985, 0.000111432734778, -0.999999979576)330.29601583, -0.00510707014965, 330.192774607

-
Components

#1: Protein
Beta-galactosidase LacZ / Beta-gal


Mass: 76938.195 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heyndrickxia coagulans (bacteria) / Gene: lacZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5JGG0, beta-galactosidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: beta-galactosidase hexamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Heyndrickxia coagulans (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 5
Buffer componentConc.: 100 mM / Name: sodium citrate / Formula: Na3(C3H5O(COO)3)
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2794
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
4cryoSPARC4.6.0CTF correction
7UCSF ChimeraX1.10.1model fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 799865
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 629632 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3TTY

3tty


Accession code: 3TTY / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 27.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005532838
ELECTRON MICROSCOPYf_angle_d0.956144550
ELECTRON MICROSCOPYf_chiral_restr0.05784566
ELECTRON MICROSCOPYf_plane_restr0.01665754
ELECTRON MICROSCOPYf_dihedral_angle_d8.37274403
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints1.03316706094E-11
ens_1d_3DDELECTRON MICROSCOPYNCS constraints1.99506247562E-12
ens_1d_4DDELECTRON MICROSCOPYNCS constraints8.46347669186E-13
ens_1d_5DDELECTRON MICROSCOPYNCS constraints1.91575398488E-12
ens_1d_6DDELECTRON MICROSCOPYNCS constraints1.55975242867E-10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more