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- PDB-8aa3: Core SusCD transporter units from the inactive levan utilisome in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aa3 | ||||||||||||
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Title | Core SusCD transporter units from the inactive levan utilisome in the presence of levan fructo-oligosaccharides DP 15-25 | ||||||||||||
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![]() | TRANSPORT PROTEIN / Membrane protein transporter / glycan transporter / SusCD / utilisome / TonB dependent transporter / TBDT / levan | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
![]() | White, J.B.R. / Silale, A. / Ranson, N.A. / van den Berg, B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 586.5 KB | Display | ![]() |
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PDB format | ![]() | 475.1 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15292MC ![]() 7znrC ![]() 7znsC ![]() 8a9yC ![]() 8aa0C ![]() 8aa1C ![]() 8aa2C ![]() 8aa4C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 65029.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / References: UniProt: Q8A6W4 #2: Protein | Mass: 115483.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / References: UniProt: Q8A6W3 #3: Polysaccharide | #4: Polysaccharide | Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #5: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 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 | ||||||||||||||||||||
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Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Supplemented with 0.5 mM levan fructo-oligosaccharides DP 15-25 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 30 mA current / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 37.8 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software | Name: RELION / Version: 3.1 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120957 / Symmetry type: POINT |