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- PDB-9sje: Cryo-EM structure of the open-closed dextran utilisome (BT3087-BT... -

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Basic information

Entry
Database: PDB / ID: 9sje
TitleCryo-EM structure of the open-closed dextran utilisome (BT3087-BT3090), with GHdex D297A E360A catalytic inactivation, with bound IMO4, IMO6, IMO7, and IMO8
Components
  • BT3088 (SGBPdex)
  • Cycloisomaltooligosaccharide glucanotransferase
  • SusC homolog
  • SusD homolog
KeywordsMEMBRANE PROTEIN / dextran / dextranase / SusD / SGBP / Bacteroides / GH / glycoside hydrolase / utilisome / GH66 / TBDT
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
SusE outer membrane protein / SusE outer membrane protein / Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain ...SusE outer membrane protein / SusE outer membrane protein / Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
SusC homolog / SusD homolog / SusE outer membrane protein domain-containing protein / Cycloisomaltooligosaccharide glucanotransferase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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 Bacteroides thetaiotaomicron
Authors: Feasey, M. / Silale, A. / Basle, A. / van den Berg, B.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusC homolog
B: SusD homolog
C: SusC homolog
D: SusD homolog
E: BT3088 (SGBPdex)
F: BT3088 (SGBPdex)
G: Cycloisomaltooligosaccharide glucanotransferase
H: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)585,91714
Polymers580,1348
Non-polymers5,7836
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules ACBDEFGH

#1: Protein SusC homolog


Mass: 110591.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3090
Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A365
#2: Protein SusD homolog


Mass: 56873.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3089
Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A366
#3: Protein BT3088 (SGBPdex)


Mass: 56086.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Carbohydrate binding modules too flexible to be resolved
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3088
Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A367
#4: Protein Cycloisomaltooligosaccharide glucanotransferase


Mass: 66515.367 Da / Num. of mol.: 2 / Mutation: D297A, E360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3087
Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A368

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Sugars , 4 types, 6 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#6: 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-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1_f6-g1_g6-h1WURCSPDB2Glycan 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]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}}}}LINUCSPDB-CARE
#7: 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-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#8: 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-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1_f6-g1WURCSPDB2Glycan 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]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE

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Details

Has ligand of interestY
Has protein modificationN

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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: Dextran utilisome of Bacteroides thetaiotaomicron, with a catalytically-inactivated GHdex, in complex with dextran
Type: COMPLEX
Details: Co-purified complex from B. theta with a His-tag on SusDdex. Dextran substrate added prior to vitrification
Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.58 MDa / Experimental value: NO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) / Strain: TDK-
Buffer solutionpH: 7.5
Details: pH 7.5 Residual LMNG (unknown %) after SEC without detergent
Buffer component
IDConc.NameBuffer-ID
110 mMHEPES1
2100 mMNaCl1
SpecimenConc.: 7.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Eluted from a single peak on a Superose 6 Increase 10/300 GL column
Specimen supportDetails: 20mA, 90 seconds per side (total 180 sec). Grids were then PEGylated: After glow discharge, grids were imported into an anaerobic glovebox and submerged in ethanol containing 5mM ...Details: 20mA, 90 seconds per side (total 180 sec). Grids were then PEGylated: After glow discharge, grids were imported into an anaerobic glovebox and submerged in ethanol containing 5mM hexa(ethylene glycol)mono-11-mercaptoundecyl ether for ~24 hours. Prior to use, grids were removed from the glovebox and successively washed three times in fresh aliquots of ethanol and left to air dry.
Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Added dextran 1.5 & 5 (0.5 mM) and Fluorinated Octyl Maltoside at 0.05% (CMC)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Krios recollection of a grid previously collected Glacios grid. Grid squares previously collected were excluded.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 23.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 481934 / Details: Blob picked
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21574 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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