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- PDB-6ytc: Solution NMR structure of the isolated NTE domain of BT1762-63 le... -
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Basic information
Entry | Database: PDB / ID: 6ytc | ||||||
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Title | Solution NMR structure of the isolated NTE domain of BT1762-63 levan transporter | ||||||
![]() | TonB-dependent receptor | ||||||
![]() | PROTEIN TRANSPORT / Glycan import / Transporter / N-terminal Domain / Ig-like fold | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Rath, P. / Mazur, A. / Hiller, S. | ||||||
![]() | ![]() Title: Insights into SusCD-mediated glycan import by a prominent gut symbiont. Authors: Declan A Gray / Joshua B R White / Abraham O Oluwole / Parthasarathi Rath / Amy J Glenwright / Adam Mazur / Michael Zahn / Arnaud Baslé / Carl Morland / Sasha L Evans / Alan Cartmell / ...Authors: Declan A Gray / Joshua B R White / Abraham O Oluwole / Parthasarathi Rath / Amy J Glenwright / Adam Mazur / Michael Zahn / Arnaud Baslé / Carl Morland / Sasha L Evans / Alan Cartmell / Carol V Robinson / Sebastian Hiller / Neil A Ranson / David N Bolam / Bert van den Berg / ![]() ![]() Abstract: In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport ...In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 623.8 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 461.7 KB | Display | ![]() |
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Full document | ![]() | 588.5 KB | Display | |
Data in XML | ![]() | 33.6 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z8iC ![]() 6z9aC ![]() 6zazC ![]() 6zltC ![]() 6zluC ![]() 6zm1C C: citing same article ( |
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Similar structure data | |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9947.120 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HMPREF2534_01945 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter, 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter_2, 1 mM U-15N, 13C-NTE Isolated NTE domain of ...Contents: 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter, 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter_2, 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter_3, 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter_4, 1 mM U-15N, 13C-NTE Isolated NTE domain of BT1762-63 levan transporter_5, 95% H2O/5% D2O Details: NMR Buffer:20 mM sodium phosphate, 150 mM NaCl and pH 7.5. Label: U-15N, 13C-NTE / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 mM / Label: NTE_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |