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- EMDB-60475: CryoEM structure of a GH1 family beta-glucosidase -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60475
TitleCryoEM structure of a GH1 family beta-glucosidase
Map data
Sample
  • Complex: dimer of GH1 family beta-glucosidase
    • Protein or peptide: Multifunctional glycoside hydrolase
Keywordsbeta-glucosidase / HYDROLASE
Function / homology
Function and homology information


glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / lactose catabolic process / glucan catabolic process / beta-galactosidase / beta-glucosidase ...glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / lactose catabolic process / glucan catabolic process / beta-galactosidase / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / protein homotrimerization / xylan catabolic process / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Multifunctional glycoside hydrolase
Similarity search - Component
Biological speciesCaldicellulosiruptor owensensis (bacteria) / Caldicellulosiruptor owensensis (strain ATCC 700167 / DSM 13100 / OL) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJiang WX / Cheng XQ / Ma LX / Cao Z / Xing Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
National Science Foundation (NSF, China)32371277 China
CitationJournal: To Be Published
Title: CryoEM structure of a GH1 family beta-glucosidase
Authors: Jiang WX / Cheng XQ / Ma LX / Cao Z / Xing Q
History
DepositionJun 7, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60475.png

Downloads & links

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Map

FileDownload / File: emd_60475.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.56 Å/pix.
x 400 pix.
= 225.333 Å		0.56 Å/pix.
x 400 pix.
= 225.333 Å		0.56 Å/pix.
x 400 pix.
= 225.333 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.056
Minimum - Maximum-0.63344383 - 0.87199014
Average (Standard dev.)0.00008785708 (±0.020187827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 225.33319 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60475_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60475_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimer of GH1 family beta-glucosidase

EntireName: dimer of GH1 family beta-glucosidase
Components
  • Complex: dimer of GH1 family beta-glucosidase
    • Protein or peptide: Multifunctional glycoside hydrolase

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Supramolecule #1: dimer of GH1 family beta-glucosidase

SupramoleculeName: dimer of GH1 family beta-glucosidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caldicellulosiruptor owensensis (bacteria)

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Macromolecule #1: Multifunctional glycoside hydrolase

MacromoleculeName: Multifunctional glycoside hydrolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: beta-glucosidase
Source (natural)Organism: Caldicellulosiruptor owensensis (strain ATCC 700167 / DSM 13100 / OL) (bacteria)
Molecular weightTheoretical: 53.501496 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSFPKGFLWG AATASYQIEG AWNEDGKGES IWDRFTHQKG NILYGHNGDV ACDHYHRHEE DVSLMKELGI KAYRFSTAWA RIFPDGFGN INQKGLEFYD KLINELVENG IEPVVTLYHW DLPQKLQDIG GWANPEIVNY YFEYAMLIIN RYKDKVKKWI T FNEPYCIA ...String:
MSFPKGFLWG AATASYQIEG AWNEDGKGES IWDRFTHQKG NILYGHNGDV ACDHYHRHEE DVSLMKELGI KAYRFSTAWA RIFPDGFGN INQKGLEFYD KLINELVENG IEPVVTLYHW DLPQKLQDIG GWANPEIVNY YFEYAMLIIN RYKDKVKKWI T FNEPYCIA FLGHWHGIHA PGIKNFKVAM DVVHNIMLSH FKVVKAVKEN NIDVEIGITL NLTPVYLQTE RLGYKVSEIE RE MVNLSSQ LDNELFLDPV LKGSYPQKLL DYLVQKDLLD SQKVNNMQQE VKENFIFPDF LGINYYTRSV RLYDENSGWI FPI RWEHPA GEYTEMGWEV FPQGLFDLLI WIKESYPQIP IYITENGAAY NDKVEDGRVH DQKRVEYLKQ HFEAARKAIK NGVD LRGYF VWSLIDNFEW AMGYTKRFGI IYVDYETQKR IKKDSFYFYQ QYIKENSLE

UniProtKB: Multifunctional glycoside hydrolase

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148229
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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