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

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Basic information

Entry
Database: PDB / ID: 9gy9
TitleThe Cryo-EM structure of bacterial beta-1,3-glucan phosphorylase from family GH161
Componentsbeta-1,3-glucan phosphorylase
KeywordsSUGAR BINDING PROTEIN / Glycoside phosphorylase / GH161 / beta-1 / 3-glucan phosphorylase
Biological speciesunclassified Bacteria (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsCioci, G. / Cooper, N. / Ladeveze, S. / Shayan, R.
Funding support France, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-1,3-glucan phosphorylase
B: beta-1,3-glucan phosphorylase


Theoretical massNumber of molelcules
Total (without water)237,9742
Polymers237,9742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 118987.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified Bacteria (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: GH161_MS (metanode satellite) Homodimeric enzyme / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacteria (eubacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21 (DE3)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethaneTris1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 12 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 38.38 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4RELION4CTF correction
7Cootmodel fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
19PHENIXmodel refinement
Image processingDetails: 1482 micrographs after discarding images with low FOM values (<10%)
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1031402 / Details: Trained topaz autopicking picking threshold 0.05
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309909 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coeficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217036
ELECTRON MICROSCOPYf_angle_d0.40323014
ELECTRON MICROSCOPYf_dihedral_angle_d9.9096338
ELECTRON MICROSCOPYf_chiral_restr0.042424
ELECTRON MICROSCOPYf_plane_restr0.0033004

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