+Open data
-Basic information
Entry | Database: PDB / ID: 6zlt | ||||||||||||||||||
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Title | Open-open state of the Bt1762-Bt1763 levan transport system | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Transporter / SusCD / Levan / TonB-dependent | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||||||||
Authors | White, J.B.R. / van den Berg, B. / Ranson, N.A. | ||||||||||||||||||
Funding support | United Kingdom, Switzerland, 5items
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Citation | Journal: Nat Commun / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zlt.cif.gz | 265.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zlt.ent.gz | 216.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zlt_validation.pdf.gz | 793.5 KB | Display | wwPDB validaton report |
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Full document | 6zlt_full_validation.pdf.gz | 806.4 KB | Display | |
Data in XML | 6zlt_validation.xml.gz | 48 KB | Display | |
Data in CIF | 6zlt_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zlt ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zlt | HTTPS FTP |
-Related structure data
Related structure data | 11273MC 6ytcC 6z8iC 6z9aC 6zazC 6zluC 6zm1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 64178.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Gene: BT_1762 / Production host: Bacteroides thetaiotaomicron (bacteria) / References: UniProt: Q8A6W4 |
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#2: Protein | Mass: 103915.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) References: UniProt: Q8A6W3 |
-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 |
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Molecular weight | Value: 0.36 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Bacteroides thetaiotaomicron (bacteria) | ||||||||||||||||||||||||
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 |
-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 |
Image recording | Electron dose: 63.84 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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 | ||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32190 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||
Atomic model building | PDB-ID: 6ZAZ |