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- EMDB-76708: Cryo-EM structure of a novel beta-galactosidase (HhGH116) from hu... -

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Basic information

Entry
Database: EMDB / ID: EMD-76708
TitleCryo-EM structure of a novel beta-galactosidase (HhGH116) from human gut
Map data
Sample
  • Complex: Epilactase HhGH116
    • Protein or peptide: Glycosyl Hydrolase family 116
KeywordsGlycosil / Hydrolase
Biological speciesmetagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsCiol H / Noske GD / Stoffel F / Morao LG / Martins MP / Murakami MT
Funding support Brazil, 5 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/09386-8 Brazil
Sao Paulo Research Foundation (FAPESP)2022/03059-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303898/2024-0 Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of a novel beta-galactosidase (HhGH116) from human gut
Authors: Ciol H / Noske GD / Stoffel F / Morao LG / Martins MP / Murakami MT
History
DepositionApr 15, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76708.png

Downloads & links

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Map

FileDownload / File: emd_76708.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.47431293 - 1.3515849
Average (Standard dev.)0.001370998 (±0.044221725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76708_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_76708_additional_1.map
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Half map: #2

Fileemd_76708_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_76708_half_map_2.map
Projections & Slices
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Sample components

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Entire : Epilactase HhGH116

EntireName: Epilactase HhGH116
Components
  • Complex: Epilactase HhGH116
    • Protein or peptide: Glycosyl Hydrolase family 116

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Supramolecule #1: Epilactase HhGH116

SupramoleculeName: Epilactase HhGH116 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 179 KDa

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Macromolecule #1: Glycosyl Hydrolase family 116

MacromoleculeName: Glycosyl Hydrolase family 116 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 89.891852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLKLKKPFKE RKSLSSPEGG ERDLALYSAF IKNGDAMNYI DISHGLGVPF GGFGTGYFVF GRHGFVNFN LDGYPEQQQT AEYPHGTLWD YTAENPDCGP VALYADIDSQ RRLLQKDSHP AIGGKPSCFV KNEVKMPYGR T VFSADDIR ...String:
MGSSHHHHHH SSGLVPRGSH MLKLKKPFKE RKSLSSPEGG ERDLALYSAF IKNGDAMNYI DISHGLGVPF GGFGTGYFVF GRHGFVNFN LDGYPEQQQT AEYPHGTLWD YTAENPDCGP VALYADIDSQ RRLLQKDSHP AIGGKPSCFV KNEVKMPYGR T VFSADDIR IELLMYSSLK RFDLSRTSIP ACVIEYTVTN TGCKSRTVSL GLAYDADRFT AGKQNGLLVL NEKSGGIAFG ID KEEPREI APGETVNYVG AIGWYYPEFV TQGLARDDII LRHNSIKDYN ENEHRKGYLR NYSLRYESAA AAAETALENY EEW KRDIDA WHSAFSFPEE TAKLLFGSYS SVITSSLHTT QGYYFEIEQP HGCLNTMDVS VYSTWLYMMN WPELEEIDLY QYIR TVPME GETRGKVWHS LWADSAHYVE EAIFVLRVWR YVLWSGNLQL AEDAWDVCKA ALEHLYSTEG SGALIDNISG NQSYD AWKM PGICNYVNNQ WLYALFSFER MSGRLGREAV VSGMKVSELL PRALKEYNEA LWDEKEGYWY AYKVTDKSNK LPFGNA VFS DQLFGFWAAS LDPEAYGILS EKQCSRALEK IYRHNRIYVP DGDYYCWLDG ALPEKEKTPS IEMNDGVYEH TGYHALC CW ICAQTGMASL MYRFGLPQTG EDVFYNVAKG IGNNHLAAGE YNRGVDGEMH AETLRYEPGK DTPRFPAYPR YKCAWEHP I SVLGLQTDLD KIYLNPAKNT DIALSEIRMG GDSLSVSVEK DWDTCLVNGK EEKPVLVRGG NKYEVEFIKT K

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 273150
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-12ri:
Cryo-EM structure of a novel beta-galactosidase (HhGH116) from human gut

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