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- PDB-9sjj: Crystal structure of SusDdex (BT3089) with bound IMO5 -

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Basic information

Entry
Database: PDB / ID: 9sjj
TitleCrystal structure of SusDdex (BT3089) with bound IMO5
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / BT3089 / SusDdex / SusD / dextran / Bacteroides / glycan-binding
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SusD homolog
Similarity search - Component
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: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,26018
Polymers53,8141
Non-polymers3,44617
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-4 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87, 106.15, 138.34
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein SusD homolog


Mass: 53814.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3089
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A366
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 326 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Lithium sulfate 0.1M Sodium acetate pH 4.5 50% w/v PEG 400 Soaked ~10 mM dextran 1.5 into grown crystals (1 crystal per drop), which cracked the large crystal. This was one fragment ...Details: 0.2M Lithium sulfate 0.1M Sodium acetate pH 4.5 50% w/v PEG 400 Soaked ~10 mM dextran 1.5 into grown crystals (1 crystal per drop), which cracked the large crystal. This was one fragment harvested for the synchrotron.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→67.29 Å / Num. obs: 70548 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Χ2: 0.99 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-67.2923.90.04470.454810.0120.0460.9799.7
1.7-1.7327.43.0151.336900.5870.8323.1290.93100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
BUSTERrefinement
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→67.288 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.813 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.082 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.191 3544 5.024 %
Rwork0.1647 67004 -
all0.166 --
obs-70548 99.991 %
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: 35.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.001 Å2-0 Å20 Å2
2--0.457 Å2-0 Å2
3---0.545 Å2
Refinement stepCycle: LAST / Resolution: 1.7→67.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 224 310 4179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123938
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.8075300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.255524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77310606
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.310188
X-RAY DIFFRACTIONr_chiral_restr0.1410.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022931
X-RAY DIFFRACTIONr_nbd_refined0.210.21938
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0640.219
X-RAY DIFFRACTIONr_mcbond_it2.913.1871847
X-RAY DIFFRACTIONr_mcangle_it3.8765.7112307
X-RAY DIFFRACTIONr_scbond_it4.7883.6152091
X-RAY DIFFRACTIONr_scangle_it6.4376.4042993
X-RAY DIFFRACTIONr_lrange_it7.35434.4466192
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
1.7-1.7440.2892530.2849360.28151890.9410.9451000.266
1.744-1.7920.2592190.2447840.2450030.9530.961000.219
1.792-1.8440.2532440.21846590.21949030.9560.9691000.192
1.844-1.9010.2192330.19445360.19547690.9690.9751000.165
1.901-1.9630.2162300.17643590.17845890.9710.981000.147
1.963-2.0320.2232450.16842420.17144880.9690.98199.97770.141
2.032-2.1080.2062220.15840890.16143110.9760.9841000.135
2.108-2.1940.1642280.14839140.14941430.9830.98799.97590.128
2.194-2.2920.1792150.14837910.1540060.9790.9871000.129
2.292-2.4030.171780.14136270.14238050.9820.9881000.123
2.403-2.5330.1651710.14634840.14736550.9830.9871000.129
2.533-2.6870.1961660.14432770.14734430.9790.9881000.131
2.687-2.8720.1791580.15831100.15932690.9790.98699.96940.148
2.872-3.1010.1831690.16728430.16830120.980.9841000.161
3.101-3.3970.21420.17526690.17728110.9770.9821000.175
3.397-3.7970.1711360.16524130.16625490.9840.9851000.172
3.797-4.3820.1541280.14121240.14122520.9880.9891000.155
4.382-5.3610.194810.14218530.14419340.9780.9891000.166
5.361-7.5570.196890.18614340.18615230.9820.9821000.212
7.557-67.2880.313370.2188600.2218970.9480.9741000.266

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