+Open data
-Basic information
Entry | Database: PDB / ID: 8aa4 | ||||||||||||
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Title | SusC components of the dextran utilisation system (utilisome) | ||||||||||||
Components | SusC homolog | ||||||||||||
Keywords | TRANSPORT PROTEIN / Membrane protein transporter / glycan transporter / SusCD / utilisome / TonB dependent transporter / TBDT | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | White, J.B.R. / Silale, A. / Ranson, N.A. / van den Berg, B. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aa4.cif.gz | 342.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aa4.ent.gz | 277.3 KB | Display | PDB format |
PDBx/mmJSON format | 8aa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aa4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8aa4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8aa4_validation.xml.gz | 60.6 KB | Display | |
Data in CIF | 8aa4_validation.cif.gz | 89.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/8aa4 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/8aa4 | HTTPS FTP |
-Related structure data
Related structure data | 15293MC 7znrC 7znsC 8a9yC 8aa0C 8aa1C 8aa2C 8aa3C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 110591.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 References: UniProt: Q8A365 |
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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 |
-Sample preparation
Component | Name: Dextran utilisation machinery (utilisome) / Type: COMPLEX Details: Sample for EM experiments was the purified dextran utilisome (Bt3088-Bt3090). Only SusC components were of sufficient resolution for model building and refinement. Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 38.78 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305372 / Symmetry type: POINT |