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Open data
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Basic information
Entry | Database: PDB / ID: 6zm1 | ||||||||||||||||||
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Title | Open-closed state of the Bt1762-Bt1763 levan transport system | ||||||||||||||||||
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![]() | MEMBRANE PROTEIN / Levan / transporter / SusCD / TonB-dependent | ||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||||||||
![]() | White, J.B.R. / van den Berg, B. / Ranson, N.A. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 678 KB | Display | ![]() |
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PDB format | ![]() | 547.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.9 KB | Display | ![]() |
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Full document | ![]() | 859.8 KB | Display | |
Data in XML | ![]() | 86.1 KB | Display | |
Data in CIF | ![]() | 128 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11277MC ![]() 6ytcC ![]() 6z8iC ![]() 6z9aC ![]() 6zazC ![]() 6zltC ![]() 6zluC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 66142.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_1762 / Production host: ![]() #2: Protein | Mass: 115483.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q8A6W3 |
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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
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Molecular weight | Value: 0.36 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.02 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 |
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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 |
Image recording | Electron dose: 63.84 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22205 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||
Atomic model building |
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