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- EMDB-76709: Cryo-EM structure of a novel beta-galactosidase (EiGH116) from an... -

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Basic information

Entry
Database: EMDB / ID: EMD-76709
TitleCryo-EM structure of a novel beta-galactosidase (EiGH116) from animal gut
Map data
Sample
  • Complex: Epilactase EiGH116
    • Protein or peptide: Glycosyl hydrolase family 116
KeywordsGlycosil / Hydrolase
Biological speciesmetagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.23 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 (EiGH116) from animal 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_76709.png

Downloads & links

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Map

FileDownload / File: emd_76709.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.3630947 - 1.1918921
Average (Standard dev.)-0.0004619646 (±0.042756252)
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_76709_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_76709_additional_1.map
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Half map: #2

Fileemd_76709_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_76709_half_map_2.map
Projections & Slices
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Sample components

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Entire : Epilactase EiGH116

EntireName: Epilactase EiGH116
Components
  • Complex: Epilactase EiGH116
    • Protein or peptide: Glycosyl hydrolase family 116

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Supramolecule #1: Epilactase EiGH116

SupramoleculeName: Epilactase EiGH116 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 171 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: 85.969453 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MNYIDISHGL GVPFGGFGTG YFVFGRHGFV NFNLDGYPEQ QQTAEYPHGT LWDYTAENPA CGPVALYAD IDAQRRLLQK DCHPKIGGKP SRFVKNEVKM PYGRTVFSAD DIRIELLMYS SLKRFDLKRT SIPACVIEYT V TNTGCKSR ...String:
MGSSHHHHHH SSGLVPRGSH MNYIDISHGL GVPFGGFGTG YFVFGRHGFV NFNLDGYPEQ QQTAEYPHGT LWDYTAENPA CGPVALYAD IDAQRRLLQK DCHPKIGGKP SRFVKNEVKM PYGRTVFSAD DIRIELLMYS SLKRFDLKRT SIPACVIEYT V TNTGCKSR TVSLGLAYDA DKLTAEKQNG LLILNEKSGG IAFGIDNEEP QEIAPGETVN YVGVIGWHYP EFVTQGIARD DI ILRHNSI KDYNENEHRK GYLRNYTLRY ESAAAAAKTA LENYEEWKRD IDAWHSAFSF PEETAKLLFG SYSSVITSSL HTT EGYYFE IEQPHGCLNT MDVSVYSTWL YMMNWPELEE IDLYQYIRTV PMEGETRGKV WHSLWADSAH YVEEAIFVLR VWRY VLWSG NLQLAEDAWD VCKAALEHLY STEGSGALID NISGNQSYDA WKMPGICNYV NNQWLYALFS FERMSGRLGR EAVVS GMKV SELLPRALKE YNEALWDEKE GYWYAYKVTD KSNKLPFGDA VFSDQLFGFW AASLDPEAYG ILSEKQCARA LEKIYR HNR IYVPDGDYYC WLDGALPEKE KTPSIEMNDG VYEHTGYHAL CCWICAQTGM ASLMYRFGLP QTGEDVFYNV AKGIGNN HL AAGEYNRGVD GEMHAETLRY EPGKDTPRFP AYPRYKCAWE HPISVLGLQT DLDKIYLNPA KNTDIALSEI RMGGDSLS V SVEKDWDTCL VNGKEEKPVL VRGGNKYEVE FIKTK

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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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k 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: 2.7 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2088909
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

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

PDB-12rj:
Cryo-EM structure of a novel beta-galactosidase (EiGH116) from animal gut

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