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- PDB-9sji: Crystal structure of SGBPdex (BT3088) with truncated residues 1-147 -

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Basic information

Entry
Database: PDB / ID: 9sji
TitleCrystal structure of SGBPdex (BT3088) with truncated residues 1-147
ComponentsBT3088 (SGBPdex)
KeywordsSUGAR BINDING PROTEIN / dextran / Bacteroides / SGBP / utilisome / glycan-binding / surface glycan binding protein / SGBPdex
Function / homologySusE outer membrane protein / SusE outer membrane protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / SusE outer membrane protein domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFeasey, M. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural and functional characterisation of the dextran utilisome from .
Authors: Matthew Feasey / Augustinas Silale / Arnaud Baslé / Bert van den Berg /
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.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BT3088 (SGBPdex)


Theoretical massNumber of molelcules
Total (without water)40,7991
Polymers40,7991
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.321, 37.549, 65.616
Angle α, β, γ (deg.)90, 100.345, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BT3088 (SGBPdex)


Mass: 40799.285 Da / Num. of mol.: 1 / Mutation: deleted residues 1-147
Source method: isolated from a genetically manipulated source
Details: N-terminal synthetic His6-tag. N-terminal truncation to remove the Ig-like NTD. All three putative carbohydrate binding modules (CBM) were included in the construct.
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3088
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A367
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD 1k 3350 35.5% w/v 200mM amino acid stock 100mM System 2 buffer (0.1M HEPES sodium salt and 0.1M MOPS at pH 7.5) pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89842 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89842 Å / Relative weight: 1
ReflectionResolution: 1.7→36.48 Å / Num. obs: 39600 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Χ2: 0.93 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-36.486.40.03430.23060.9970.020.0390.3699.1
1.7-1.7372.0630.720690.7131.2642.4240.91100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data scaling
Cootmodel building
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.477 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.605 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.27 2011 5.081 %
Rwork0.1982 37564 -
all0.202 --
obs-39575 99.929 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.417 Å2
Baniso -1Baniso -2Baniso -3
1--3.752 Å2-0 Å21.644 Å2
2--0.982 Å2-0 Å2
3---2.034 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 0 347 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122816
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162540
X-RAY DIFFRACTIONr_angle_refined_deg2.2141.8133826
X-RAY DIFFRACTIONr_angle_other_deg0.8991.7595888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7685349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.18357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47710460
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.57110128
X-RAY DIFFRACTIONr_chiral_restr0.1160.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023319
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02635
X-RAY DIFFRACTIONr_nbd_refined0.2080.2592
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22551
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21363
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.222
X-RAY DIFFRACTIONr_nbd_other0.1430.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.219
X-RAY DIFFRACTIONr_mcbond_it4.8764.0031399
X-RAY DIFFRACTIONr_mcbond_other4.8684.0031399
X-RAY DIFFRACTIONr_mcangle_it6.0297.1811747
X-RAY DIFFRACTIONr_mcangle_other6.0317.1831748
X-RAY DIFFRACTIONr_scbond_it6.2324.3911417
X-RAY DIFFRACTIONr_scbond_other6.234.3911417
X-RAY DIFFRACTIONr_scangle_it8.5557.8542079
X-RAY DIFFRACTIONr_scangle_other8.5537.8552080
X-RAY DIFFRACTIONr_lrange_it29.70547.7363344
X-RAY DIFFRACTIONr_lrange_other28.98846.5123276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.4381320.42527250.42628630.8390.8299.79040.414
1.744-1.7920.3941440.38927170.3928620.8380.85199.96510.374
1.792-1.8440.361580.34325610.34427220.8630.87499.88980.318
1.844-1.90.3491330.34925400.34926740.8730.88199.96260.327
1.9-1.9620.3691180.30824820.31126030.8910.90299.88480.288
1.962-2.0310.3071290.25223580.25524910.9270.94899.83940.232
2.031-2.1070.2841360.23822860.2424230.9380.95899.95870.218
2.107-2.1930.3051220.23422180.23723410.9270.9699.95730.213
2.193-2.290.2911100.19821140.20322250.9440.97399.95510.179
2.29-2.4020.2861050.20220270.20621330.9430.97299.95310.182
2.402-2.5310.3221010.19919700.20420710.9360.9741000.183
2.531-2.6840.296960.20418330.20819300.9470.97499.94820.189
2.684-2.8680.3940.20117350.20718290.9390.9731000.19
2.868-3.0960.279840.20416160.20817000.9470.9741000.196
3.096-3.3890.29720.20614950.2115670.9480.9741000.204
3.389-3.7850.271790.18313630.18714420.9610.9821000.184
3.785-4.3630.253650.14311950.14812610.9650.98899.92070.152
4.363-5.3240.147520.1210340.12210860.9880.9931000.131
5.324-7.450.211520.1398060.1448580.9790.9891000.145
7.45-36.4770.195290.1344890.1375180.9820.9881000.141

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