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- EMDB-54945: Cryo-EM structure of the open-closed dextran utilisome (BT3087-BT... -

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Basic information

Entry
Database: EMDB / ID: EMD-54945
TitleCryo-EM structure of the open-closed dextran utilisome (BT3087-BT3090), with GHdex D297A E360A catalytic inactivation, with bound IMO4, IMO6, IMO7, and IMO8
Map data
Sample
  • Complex: Dextran utilisome of Bacteroides thetaiotaomicron, with a catalytically-inactivated GHdex, in complex with dextran
    • Protein or peptide: SusC homolog
    • Protein or peptide: SusD homolog
    • Protein or peptide: BT3088 (SGBPdex)
    • Protein or peptide: Cycloisomaltooligosaccharide glucanotransferase
Keywordsdextran / dextranase / SusD / SGBP / Bacteroides / GH / glycoside hydrolase / utilisome / GH66 / MEMBRANE PROTEIN / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFeasey M / Basle A / van den Berg B
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54945.png

Downloads & links

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Map

FileDownload / File: emd_54945.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.4 Å		0.83 Å/pix.
x 400 pix.
= 332.4 Å		0.83 Å/pix.
x 400 pix.
= 332.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.09094138 - 0.18667774
Average (Standard dev.)0.00034818082 (±0.0062833955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54945_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54945_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dextran utilisome of Bacteroides thetaiotaomicron, with a catalyt...

EntireName: Dextran utilisome of Bacteroides thetaiotaomicron, with a catalytically-inactivated GHdex, in complex with dextran
Components
  • Complex: Dextran utilisome of Bacteroides thetaiotaomicron, with a catalytically-inactivated GHdex, in complex with dextran
    • Protein or peptide: SusC homolog
    • Protein or peptide: SusD homolog
    • Protein or peptide: BT3088 (SGBPdex)
    • Protein or peptide: Cycloisomaltooligosaccharide glucanotransferase

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Supramolecule #1: Dextran utilisome of Bacteroides thetaiotaomicron, with a catalyt...

SupramoleculeName: Dextran utilisome of Bacteroides thetaiotaomicron, with a catalytically-inactivated GHdex, in complex with dextran
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Co-purified complex from B. theta with a His-tag on SusDdex. Dextran substrate added prior to vitrification
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) / Strain: TDK-
Molecular weightTheoretical: 580 KDa

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Macromolecule #1: SusC homolog

MacromoleculeName: SusC homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 110.591242 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MEQSIKSKGF EHRLLLIMWG LLLSLSAFAQ QITVKGHVVD ATGEPVIGAS VIEGKSTNGT ITDIDGNFSL NVSANSALTI SFVGYKTQT VSVNGKTALK VTLQEDTEVL DEVVVVGYGT MKKSDLTGAV SSVGVKDIKD SPVANIGQAM QGKVSGVQII D AGKPGDNV ...String:
MEQSIKSKGF EHRLLLIMWG LLLSLSAFAQ QITVKGHVVD ATGEPVIGAS VIEGKSTNGT ITDIDGNFSL NVSANSALTI SFVGYKTQT VSVNGKTALK VTLQEDTEVL DEVVVVGYGT MKKSDLTGAV SSVGVKDIKD SPVANIGQAM QGKVSGVQII D AGKPGDNV TIKIRGLGTI NNSNPLVVID GIPTDLGLSS LNMADVERVD VLKDASATAI YGSRGANGVV MITSKRGAEG AG KVTVNAN WAIQNATKVP DMLNAAQYAA LSNDMLSNND DNTNPYWADP SSLGKGTNWL DEMLRTGVKQ SYSVSYSGGT EKA HYYVSG GFLDQSGIVK SVNYRRFNFQ ANSDAQVNKW LKFTTNLTFS TDVKEGGTYS IGDAMKALPT QPVKNDDGSW SGPG QEAQW YGSIRNPIGT LHMMTNETKG YNFLANITGE ITFTKWLKLK STFGYDAKFW FADNFTPAYD WKPNPVEESS RYKSD NKSF TYLWDNYFVF DHTFAKKHRV GVMAGSSAQW NNYDYLNAQK NIFMFDNIHE MDNGEKMYSL GGSQSDWALL SLMARL NYS YEDKYLLTAT VRRDGSSRFG KNNRWGTFPS VSLAWRVSQE DWFPKDNFLM NDLKLRVGYG VTGNQEIGNY GFVASYN TG VYPFGNNNST ALVSTTLSNP NIHWEEVRQA NFGVDMSLFD SRVSLSLDAY IKNTNDMLVK ASIPITSGFE DTTETFTN A GKMRNKGVEM TLRTINLKGI FSWESALTAT YNKNEILDLN SETPMFINQI GNSYVTMLKA GYPINVFYGY VTDGLFQNW GEVNRHATQP GAAPGDIRFR DLNNDGVIND EDRTILGNPN PNWFFSLSNN LSYKGWELSV FLQGVAGNKI YNANNVDNEG MAAAYNQTT AVLNRWTGEG TSYSMPRAIW GDPNQNCRVS DRFVENGSYL RLKNITLSYT LPKKWLQKIQ LENARISFSC E NVATITRY SGFDPEVDVN GIDSSRYPIS RTFSMGLNFN F

UniProtKB: SusC homolog

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Macromolecule #2: SusD homolog

MacromoleculeName: SusD homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 56.873871 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MKKKLTFIMI LAVLALTSCS DFLDKYPKYG VDPESEVTNE IAVALTTACY KTLQSSNMYN QRLWSLDILA GNSEVGAGGG TDGLETVQA ANFIAQSDNG FALYVWRSPW VGIGRCNIVL SNLPSAAISD EIKDRCMGEA YFLRAHYYYI LVRLYGGVPL R LQPFEPGQ ...String:
MKKKLTFIMI LAVLALTSCS DFLDKYPKYG VDPESEVTNE IAVALTTACY KTLQSSNMYN QRLWSLDILA GNSEVGAGGG TDGLETVQA ANFIAQSDNG FALYVWRSPW VGIGRCNIVL SNLPSAAISD EIKDRCMGEA YFLRAHYYYI LVRLYGGVPL R LQPFEPGQ STDIARNTVD EVYAQILSDC KNAVDMLPPK SSYGENDKGR ACKEAAMAML ADIYLTLAPN HRDYYNEVVT LC DQITAMG YDLSQCKYAD NFDATINNGA ESLFEVQYSG STEYDFWGGD NQSSWLSTFM GPRNSGMVAG AYGWNLPTEE FIK EYEAGD LRKDVTVLYQ GCPAFDGMEY RRSWSNTGYN VRKFLVSKTV SPEYNTNPNN FVVYRYADVL LKKAEALNEL GHPD QAAAP LNIVRQRAGL ADVPTTLNQE TMREKIIHER RMELAFEGHR WFDMIRINNG NYAIEFLKSI GKNQVTKERL LLPIP QTEM DSNNLMTQNP GYAAAAHHHH HH

UniProtKB: SusD homolog

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Macromolecule #3: BT3088 (SGBPdex)

MacromoleculeName: BT3088 (SGBPdex) / type: protein_or_peptide / ID: 3
Details: Carbohydrate binding modules too flexible to be resolved
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 56.086352 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MKKYIYQILC SLFIGGAMVS CAEDYMETDK GHDTLTLTVN QQEIVLNEKN HTQEALTLSW TTGTNYGSGN RISYTLEIAK AGTDFARAY SVDLGTGTYQ WTKKTEELNQ FLNTQLGVGY AEKVSLEARI TATVAGMEEK EQRATVALDV TTYQPVTPTL Y LIGEAAPN ...String:
MKKYIYQILC SLFIGGAMVS CAEDYMETDK GHDTLTLTVN QQEIVLNEKN HTQEALTLSW TTGTNYGSGN RISYTLEIAK AGTDFARAY SVDLGTGTYQ WTKKTEELNQ FLNTQLGVGY AEKVSLEARI TATVAGMEEK EQRATVALDV TTYQPVTPTL Y LIGEAAPN GWSADQATPM ERTDNGQFTW TGKLNTGVFK FITTLGEFLP SYNRDAAAGE ELRLIYRTSG DEPDEPFTVS KE ATYIVKV DLLDLTMTMT ETENIGWRFE EFYIVGSFTG DNGWGFEALS KDAVQMNLFH YGAVIPWKAD GDFKFTSVTD FGQ SDAFFH PTEGNAPYTS TSVVLGGEDN KWQMKESECG KAYKVLFLTA KGKEKMLMRP FTPYEGLYLV GDATPNGWSI DNAT PMAKS ADSPYIFTWS GTLNTGEMKI SCDKQSDWNG DWLMADKSGK APTGEVETAL FTSKTDAELK NMYPDTDLGS LDNKW NIQE AGSYRITIDQ LKETISIVKQ

UniProtKB: SusE outer membrane protein domain-containing protein

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Macromolecule #4: Cycloisomaltooligosaccharide glucanotransferase

MacromoleculeName: Cycloisomaltooligosaccharide glucanotransferase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 66.515367 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MKKIIYLVAA FLCLSCSDDH ESNPQNGGAS GSVTEVTPVT SDLCVELTTD KAFYKPNETV TFTAADALPA GTKVRYRLLG EIVGEEPVS GTNWTWKAPS TDFKGYMAEL YRQENGTDVI VGTIAVDVSS HPARFPRYGF VADFDGVKTE EKTLEEMAYL N RHHINWVQ ...String:
MKKIIYLVAA FLCLSCSDDH ESNPQNGGAS GSVTEVTPVT SDLCVELTTD KAFYKPNETV TFTAADALPA GTKVRYRLLG EIVGEEPVS GTNWTWKAPS TDFKGYMAEL YRQENGTDVI VGTIAVDVSS HPARFPRYGF VADFDGVKTE EKTLEEMAYL N RHHINWVQ FQDWHNKHHW PLGGTRTQLD EEYLDIANRP VHTSSVKNYI KAQQHFGMKS MFYNLCFGAL KDAASDGVKE EW YLFKDAS HTTKDSHDLP SGWKSNIYLV DPSDKEWQQY MAERNDDVYA NFAFDGYQIA QLGKRGTLYN YNGTPVNLRE GYA SFIEAM KQAHPDKSLV MNAVSRYGAR QIGETGKVDF FYNAMWADEA DFTHLKAVLY ENGVYGNNQL NTVFAAYMNY NKAD HRGEF NTAGILLTDA VMFALGGSHL ELGGDHMLCK EYFPNDNLTM SEELKTAMVH YYDFLTSYQN LLRDGGTENS IAMNC TNGE MKLNVWPPKL GSVTTYAKQV DGKQVVHLLN FSQANSLSWR DVDGTMPEPA LITKATLQMN LPAKVNKLWV ASPDVH GGA LQELAFTQEN GVVSFTLPAL KYWTMIVAE

UniProtKB: Cycloisomaltooligosaccharide glucanotransferase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7.5 mg/mL
BufferpH: 7.5 / Component:
ConcentrationName
10.0 mMHEPES
100.0 mMNaCl

Details: pH 7.5 Residual LMNG (unknown %) after SEC without detergent
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
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 ...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.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Added dextran 1.5 & 5 (0.5 mM) and Fluorinated Octyl Maltoside at 0.05% (CMC).
DetailsEluted from a single peak on a Superose 6 Increase 10/300 GL column

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Electron microscopy

MicroscopeTFS KRIOS
DetailsKrios recollection of a grid previously collected Glacios grid. Grid squares previously collected were excluded.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 23.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 481934 / Details: Blob picked
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Pre-deposition X-ray models, Alphafold prediction, PDB 8AA4
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21574
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10
FSC plot (resolution estimation)

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