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- EMDB-19123: cyclic b-1,2-glucan synthase IGT mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-19123
Titlecyclic b-1,2-glucan synthase IGT mutant
Map data
Sample
  • Complex: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
Keywordscgs / cyclic glucan / ANTIBIOTIC
Biological speciesAgrobacterium tumefaciens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.99 Å
AuthorsSedzicki J / Ni D / Lehmann F / Stahlberg H / Dehio C
Funding support Switzerland, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_201273 Switzerland
Swiss National Science FoundationNCCR AntiResist grant 180541 Switzerland
Swiss National Science FoundationCRSII5_177195 Switzerland
Swiss National Science FoundationSino-Swiss Science and Technology Cooperation SSSTC grant Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens.
Authors: Jaroslaw Sedzicki / Dongchun Ni / Frank Lehmann / Henning Stahlberg / Christoph Dehio /
Abstract: The synthesis of complex sugars is a key aspect of microbial biology. Cyclic β-1,2-glucan (CβG) is a circular polysaccharide critical for host interactions of many bacteria, including major ...The synthesis of complex sugars is a key aspect of microbial biology. Cyclic β-1,2-glucan (CβG) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). CβG is produced by the cyclic glucan synthase (Cgs), a multi-domain membrane protein. So far, its structure as well as the mechanism underlining the synthesis have not been clarified. Here we use cryo-electron microscopy (cryo-EM) and functional approaches to study Cgs from A. tumefaciens. We determine the structure of this complex protein machinery and clarify key aspects of CβG synthesis, revealing a distinct mechanism that uses a tyrosine-linked oligosaccharide intermediate in cycles of polymerization and processing of the glucan chain. Our research opens possibilities for combating pathogens that rely on polysaccharide virulence factors and may lead to synthetic biology approaches for producing complex cyclic sugars.
History
DepositionDec 12, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19123.png

Downloads & links

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Map

FileDownload / File: emd_19123.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.476 Å
Density
Contour LevelBy AUTHOR: 0.402
Minimum - Maximum-2.204716 - 4.4207935
Average (Standard dev.)0.0026238929 (±0.09003288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 369.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19123_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19123_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 : cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens

EntireName: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
Components
  • Complex: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens

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Supramolecule #1: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens

SupramoleculeName: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19465
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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