Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Structural and functional characterisation of the dextran utilisome from .
Journal, issue, pages	J Struct Biol X, Vol. 14, Page 100153, Year 2026
Publish date	Jul 17, 2026
Authors	Matthew Feasey / Augustinas Silale / Arnaud Baslé / Bert van den Berg /
PubMed Abstract	() is a model Bacteroidota of the healthy human gut microbiota and a specialist in glycan utilisation. Like other , has many highly regulated polysaccharide utilisation loci (PUL) that encode outer ... () is a model Bacteroidota of the healthy human gut microbiota and a specialist in glycan utilisation. Like other , has many highly regulated polysaccharide utilisation loci (PUL) that encode outer membrane (OM) TonB-dependent transporters (SusC), closely associated "lid" lipoproteins (SusD), and additional surface-exposed lipoproteins (SLPs) that bind and partially degrade specific glycans derived from host cells, diet, or other microbiota members. The canonical starch PUL products are thought to form a dynamic complex in the presence of starch. However, other PULs form stable complexes in the absence of substrate (recently named "utilisomes"), with additional surface lipoproteins tightly associated with the core SusCD complex. In this study, we characterised the dextran utilisome, with a SusCD core and an associated glycoside hydrolase (GH) and surface glycan binding protein (SBGP). Via X-ray crystallography we solved high-resolution structures of SBGP in isolation and SusD and GH bound to dextran oligosaccharides. We used isothermal titration calorimetry (ITC) to quantify ligand binding of wild type and mutant SLPs. We further used single particle cryo-EM of the catalytically inactive dextran utilisome to visualise open and closed states of the complex. Three occupied dextran binding sites were observed across SusC, SusD and GH, with substrate observed in both open and closed states of SusD. 3D variability analysis showed a minority of particles in the process of SusD lid closure. Together our work defines commonalities and differences across utilisomes dedicated to the import of simple glycans.
External links	J Struct Biol X / PubMed:42569704 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.65 - 2.9 Å
Structure data	54945 9sje EMDB-54945, PDB-9sje: Cryo-EM structure of the open-closed dextran utilisome (BT3087-BT3090), with GHdex D297A E360A catalytic inactivation, with bound IMO4, IMO6, IMO7, and IMO8 Method: EM (single particle) / Resolution: 2.9 Å 55024 9sm2 EMDB-55024, PDB-9sm2: Cryo-EM structure of the closed-closed dextran utilisome (BT3087-BT3090), with GHdex D297A E360A catalytic inactivation, with bound IMO4, IMO6 and IMO8 Method: EM (single particle) / Resolution: 2.5 Å PDB-9sjf: Crystal structure of GHdex dextranase (BT3087), E360A catalytic mutant with bound IMO3 Method: X-RAY DIFFRACTION / Resolution: 2.2 Å PDB-9sjg: Crystal structure of apo GHdex dextranase (BT3087), wild type Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-9sjh: Crystal structure of apo GHdex dextranase (BT3087), E360A catalytic mutant Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-9sji: Crystal structure of SGBPdex (BT3088) with truncated residues 1-147 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-9sjj: Crystal structure of SusDdex (BT3089) with bound IMO5 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-9sjk: Crystal structure of apo SusDdex (BT3089) Method: X-RAY DIFFRACTION / Resolution: 1.65 Å
Chemicals	ChemComp-CL: Unknown entry ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER ChemComp-MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH bufferYM ChemComp-NA: Unknown entry ChemComp-PG4: TETRAETHYLENE GLYCOL / precipitantYM ChemComp-1PE: PENTAETHYLENE GLYCOL / precipitantYM ChemComp-PEG: DI(HYDROXYETHYL)ETHER ChemComp-P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / precipitantYM ChemComp-PGE: TRIETHYLENE GLYCOL
Source	bacteroides thetaiotaomicron vpi-5482 (bacteria)
Keywords	MEMBRANE PROTEIN / dextran / dextranase / SusD / SGBP / Bacteroides / GH / glycoside hydrolase / utilisome / GH66 / TBDT / SUGAR BINDING PROTEIN / enzyme / glycan-binding / surface glycan binding protein / SGBPdex / BT3089 / SusDdex