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- EMDB-51692: The Cryo-EM structure of bacterial beta-1,3-glucan phosphorylase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-51692
TitleThe Cryo-EM structure of bacterial beta-1,3-glucan phosphorylase from family GH161
Map data
Sample
  • Complex: GH161_MS (metanode satellite) Homodimeric enzyme
    • Protein or peptide: beta-1,3-glucan phosphorylase
KeywordsGlycoside phosphorylase / GH161 / beta-1 / 3-glucan phosphorylase / SUGAR BINDING PROTEIN
Biological speciesBacteria (eubacteria) / unclassified Bacteria (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsCioci G / Cooper N / Ladeveze S / Shayan R
Funding support France, 1 items
OrganizationGrant numberCountry
Not funded France
CitationJournal: To Be Published
Title: The Cryo-EM structure of bacterial beta-1,3-glucan phosphorylase from family GH161
Authors: Cioci G / Cooper N / Ladeveze S / Shayan R
History
DepositionOct 2, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51692.png

Downloads & links

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Map

FileDownload / File: emd_51692.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.012009951 - 0.042863343
Average (Standard dev.)-0.00009760431 (±0.0018899748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51692_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_51692_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 : GH161_MS (metanode satellite) Homodimeric enzyme

EntireName: GH161_MS (metanode satellite) Homodimeric enzyme
Components
  • Complex: GH161_MS (metanode satellite) Homodimeric enzyme
    • Protein or peptide: beta-1,3-glucan phosphorylase

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Supramolecule #1: GH161_MS (metanode satellite) Homodimeric enzyme

SupramoleculeName: GH161_MS (metanode satellite) Homodimeric enzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteria (eubacteria)

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Macromolecule #1: beta-1,3-glucan phosphorylase

MacromoleculeName: beta-1,3-glucan phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: unclassified Bacteria (bacteria)
Molecular weightTheoretical: 118.987039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ETFVMDDYGK KSTFASFLPG IAGIRGIPIW CYYVNRGQCV VSFGVDNKDH AIMEFYPAHQ AYQNVKTTGF RTFLKKNGTV FEPFSDENI THRMQIHMNG LAIEEQNRSS GMDTKVVYYT LPGENVGALV RVVSVTNQSG EPIELELIDG MPAVIPYGVS M DSMKNMGQ ...String:
ETFVMDDYGK KSTFASFLPG IAGIRGIPIW CYYVNRGQCV VSFGVDNKDH AIMEFYPAHQ AYQNVKTTGF RTFLKKNGTV FEPFSDENI THRMQIHMNG LAIEEQNRSS GMDTKVVYYT LPGENVGALV RVVSVTNQSG EPIELELIDG MPAVIPYGVS M DSMKNMGQ TAKAWMQVED LSEGLPYYRV RASMDDTAAV RRIDGGNFSA CCEADGRRLQ PIVDPSLIFS YDLSLKRPVG FE ERPLKEL LLEEQMTQNL LPCSFYGITR TLAPGGSVTL YELIGQVENK QLLKEYFAEK KDAAYFEAKK READELAEAL TDG IRTRTA SAAFDAYCRY TYMDNVLRGG YPMQLGNNKI FYVYSRKHGD LERDYNYFSM LPEFYSQGNG NFRDVNQNRR CDTF FAPFV GRKNIQEFYS LIQLDGYNPL GVEKLTYRLS KERAKKLLTD VKEEQRSALI DFATKPFTPG ALCRKFGEVF GDTWD ETLF IRVIDFAEEM VNGSFGEGYW SDHWTYNLDL ILDYLSVFPE QEKEMLYEEV YTTFLSRINV NRRFRRYVET ENGLRQ YRA LNEASRRAAA AEKLVRTEYG SGDVLTMTLM EKLILLGAVK FATLDAYGMG IEMEGGKPGW YDALNGMPGL FGSSMAE TY ELARMLSYTI EALKQYPGEV ALIEELGCFL DELNLITRLE HDNIMRDEEL LSFWNRINDA KEIYRDKTYQ GVSGKKMV Y HTEQLAAILE GFLEIVTCGI KKARRISGEI CPTYFTYEVP EYEKLKDGGI RPLKFVPQNM PYFLEGPVRY LKLPVEQGE KRALYEAVKE SDLYDGELSM YKVNASLADS SFELGRARAF TPGWLENESI WLHMEYKYLL ELLRSGLYEE FFADFKKAAI PFQNPEIYG RSIYENSSFI ASSRNPNPSC RGRGFVARLS GSTIEFISMW KEMMFGAHPF RTEQEELVFS LAPAIPAYLI P EDGRLSAA FMSKTTVCYE FGGHRDYVPG TYRIRHMVFF YENGSQATVE GEKVSGKLAE DIRAGRVRKM EVAVDLEHHH H

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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 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTristris(hydroxymethyl)aminomethane
150.0 mMNaClSodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 12 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 38.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Details1482 micrographs after discarding images with low FOM values (<10%)
Particle selectionNumber selected: 1031402 / Details: Trained topaz autopicking picking threshold 0.05
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 309909
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coeficient
Output model

PDB-9gy9:
The Cryo-EM structure of bacterial beta-1,3-glucan phosphorylase from family GH161

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