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- PDB-8aa3: Core SusCD transporter units from the inactive levan utilisome in... -

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Basic information

Entry
Database: PDB / ID: 8aa3
TitleCore SusCD transporter units from the inactive levan utilisome in the presence of levan fructo-oligosaccharides DP 15-25
Components
  • SusC homolog
  • SusD homolog
KeywordsTRANSPORT PROTEIN / Membrane protein transporter / glycan transporter / SusCD / utilisome / TonB dependent transporter / TBDT / levan
Function / homology
Function and homology information


cell outer membrane / membrane / metal ion binding
Similarity search - Function
TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / CarboxypepD_reg-like domain / 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 outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / CarboxypepD_reg-like domain / 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-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
SusC homolog / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWhite, J.B.R. / Silale, A. / Ranson, N.A. / van den Berg, B.
Funding support United Kingdom, 3items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: SusD homolog
A: SusC homolog
J: SusD homolog
I: SusC homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,76212
Polymers361,0264
Non-polymers3,7368
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein SusD homolog


Mass: 65029.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / References: UniProt: Q8A6W4
#2: Protein SusC homolog


Mass: 115483.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / References: UniProt: Q8A6W3
#3: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DFrufb2-6DFrufb2-6DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[ha122h-2b_2-5]/1-1-1-1/a6-b2_b6-c2_c6-d2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D- ...beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-[beta-D-fructofuranose-(2-1)]beta-D-fructofuranose-(2-6)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-6DFrufb2-6DFrufb2-6DFrufb2-6[DFrufb2-1]DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[ha122h-2b_2-5]/1-1-1-1-1-1-1/a6-b2_b1-c2_b6-d2_d6-e2_e6-f2_f6-g2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}}}}}LINUCSPDB-CARE
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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: Inactive levan utilisation machinery (utilisome) in the presence of fructo-oligosaccharides DP 15-25
Type: COMPLEX
Details: Sample for EM experiments was the purified levan utilisome (Bt1760-Bt1763). Particle subtraction and focused refinement were used to generate a map of the core SusC2D2 transport unit with ...Details: Sample for EM experiments was the purified levan utilisome (Bt1760-Bt1763). Particle subtraction and focused refinement were used to generate a map of the core SusC2D2 transport unit with bound fructo-oligosaccharides.
Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Source (recombinant)Organism: Bacteroides thetaiotaomicron (bacteria)
Buffer solutionpH: 7.5
Details: Supplemented with 0.5 mM levan fructo-oligosaccharides DP 15-25
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMSodium ChlorideNaCl1
30.03 % (w/v)DDM1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA current / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 37.8 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120957 / Symmetry type: POINT

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