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- EMDB-15293: Consensus reconstruction of the dextran utilisation system -

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Basic information

Entry
Database: EMDB / ID: EMD-15293
TitleConsensus reconstruction of the dextran utilisation system
Map data
Sample
  • Complex: Dextran utilisation machinery (utilisome)
    • Protein or peptide: SusC homolog
KeywordsMembrane protein transporter / glycan transporter / SusCD / utilisome / TonB dependent transporter / TBDT / TRANSPORT PROTEIN
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / 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
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWhite JBR / Silale A / Ranson NA / van den Berg B
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust215064/Z/18/Z United Kingdom
Wellcome Trust214222/Z/18/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Nature / Year: 2023
Title: Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes.
Authors: Joshua B R White / Augustinas Silale / Matthew Feasey / Tiaan Heunis / Yiling Zhu / Hong Zheng / Akshada Gajbhiye / Susan Firbank / Arnaud Baslé / Matthias Trost / David N Bolam / Bert van ...Authors: Joshua B R White / Augustinas Silale / Matthew Feasey / Tiaan Heunis / Yiling Zhu / Hong Zheng / Akshada Gajbhiye / Susan Firbank / Arnaud Baslé / Matthias Trost / David N Bolam / Bert van den Berg / Neil A Ranson /
Abstract: Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut. Glycan uptake across the bacterial outer membrane of these bacteria ...Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut. Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome.
History
DepositionJun 29, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15293.png

Downloads & links

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Map

FileDownload / File: emd_15293.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0164
Minimum - Maximum-0.018345067 - 0.050372407
Average (Standard dev.)0.0002893685 (±0.0016445842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15293_msk_1.map
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Additional map: #1

Fileemd_15293_additional_1.map
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Half map: #1

Fileemd_15293_half_map_1.map
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Half map: #2

Fileemd_15293_half_map_2.map
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Sample components

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Entire : Dextran utilisation machinery (utilisome)

EntireName: Dextran utilisation machinery (utilisome)
Components
  • Complex: Dextran utilisation machinery (utilisome)
    • Protein or peptide: SusC homolog

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Supramolecule #1: Dextran utilisation machinery (utilisome)

SupramoleculeName: Dextran utilisation machinery (utilisome) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sample for EM experiments was the purified dextran utilisome (Bt3088-Bt3090). Only SusC components were of sufficient resolution for model building and refinement.
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)

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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)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Molecular weightTheoretical: 110.591242 KDa
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
10.0 mMHEPES
100.0 mMSodium chlorideNaCl
0.03 % (w/v)DDM
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 38.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 305372
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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