8RF0 | pdb_00008rf0

WT-CGS sample in nanodisc

• PDB DOI: https://doi.org/10.2210/pdb8RF0/pdb
• EM Map EMD-19114: EMDB EMDataResource

• Classification: ANTIBIOTIC
• Organism(s): Agrobacterium tumefaciens
• Expression System: Agrobacterium tumefaciens
• Mutation(s): No 


• Deposited: 2023-12-12 Released: 2024-03-20 
• Deposition Author(s): Sedzicki, J., Ni, D., Lehmann, F., Stahlberg, H., Dehio, C.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-function analysis of the cyclic beta-1,2-glucan synthase from Agrobacterium tumefaciens.

Sedzicki, J., Ni, D., Lehmann, F., Stahlberg, H., Dehio, C.

(2024) Nat Commun 15: 1844

• PubMed: 38418509 
• DOI: https://doi.org/10.1038/s41467-024-45415-8


• PubMed 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 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.

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Organizational Affiliation: 
• Biozentrum, University of Basel, Basel, CH-4056, Switzerland.
Laboratory of Biological Electron Microscopy (LBEM), IPHYS, SB, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, CH-1015, Switzerland.
Laboratory of Biological Electron Microscopy (LBEM), IPHYS, SB, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, CH-1015, Switzerland. [e-mail].
Biozentrum, University of Basel, Basel, CH-4056, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 318.97 kDa 
• Atom Count: 21,922 
• Modeled Residue Count: 2,780 
• Deposited Residue Count: 2,818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic beta-(1,2)-glucan synthase NdvB	A	2,818	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: ndvB, AGTUEHA105_LOCUS2378

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	B	9		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	C	9		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	D [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Sedzicki, J., Ni, D., Lehmann, F., Stahlberg, H., Dehio, C.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_201273
Swiss National Science Foundation	Switzerland	NCCR AntiResist grant 180541
Swiss National Science Foundation	Switzerland	CRSII5_177195
Swiss National Science Foundation	Switzerland	Sino-Swiss Science and Technology Cooperation SSSTC grant

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Data collection, Structure summary