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- PDB-8rfg: CgsiGP3 sample in nanodisc -

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Basic information

Entry
Database: PDB / ID: 8rfg
TitleCgsiGP3 sample in nanodisc
ComponentsCyclic beta 1-2 glucan synthetase
KeywordsANTIBIOTIC / cgs / cyclic glucan
Function / homology
Function and homology information


cellobiose phosphorylase / cellobiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process / membrane
Similarity search - Function
NdvB, GH94N domain 1 / NdvB, GH94N domain 2 / Glycoamylase-like, conserved domain / Putative glucoamylase / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain ...NdvB, GH94N domain 1 / NdvB, GH94N domain 2 / Glycoamylase-like, conserved domain / Putative glucoamylase / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Cyclic beta 1-2 glucan synthetase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsSedzicki, J. / Ni, D. / Lehmann, F. / Stahlberg, H. / Dehio, C.
Funding support Switzerland, 4items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic beta 1-2 glucan synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,7914
Polymers313,3591
Non-polymers4,4323
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9230 Å2
ΔGint107 kcal/mol
Surface area111010 Å2
MethodPISA

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Components

#1: Protein Cyclic beta 1-2 glucan synthetase


Mass: 313358.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Agrobacterium tumefaciens (bacteria) / References: UniProt: A0A0F4FQW4, cellobiose phosphorylase
#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2125.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,13,12/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1_g2-h1_h2-i1_i2-j1_j2-k1_k2-l1_l2-m1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98115 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422385
ELECTRON MICROSCOPYf_angle_d0.64130427
ELECTRON MICROSCOPYf_dihedral_angle_d4.2773062
ELECTRON MICROSCOPYf_chiral_restr0.0423436
ELECTRON MICROSCOPYf_plane_restr0.0053930

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