6YTC | pdb_00006ytc

Solution NMR structure of the isolated NTE domain of BT1762-63 levan transporter


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 6YTC

This is version 1.3 of the entry. See complete history

Literature

Insights into SusCD-mediated glycan import by a prominent gut symbiont.

Gray, D.A.White, J.B.R.Oluwole, A.O.Rath, P.Glenwright, A.J.Mazur, A.Zahn, M.Basle, A.Morland, C.Evans, S.L.Cartmell, A.Robinson, C.V.Hiller, S.Ranson, N.A.Bolam, D.N.van den Berg, B.

(2021) Nat Commun 12: 44-44

  • DOI: https://doi.org/10.1038/s41467-020-20285-y
  • Primary Citation Related Structures: 
    6YTC, 6Z8I, 6Z9A, 6ZAZ, 6ZLT, 6ZLU, 6ZM1

  • PubMed 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 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.


  • Organizational Affiliation
    • Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.

Macromolecule Content 

  • Total Structure Weight: 9.95 kDa 
  • Atom Count: 698 
  • Modeled Residue Count: 93 
  • Deposited Residue Count: 93 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TonB-dependent receptor93Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: HMPREF2534_01945
UniProt
Find proteins for Q8A6W3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A6W3 
Go to UniProtKB:  Q8A6W3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A6W3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2024-06-19
    Changes: Data collection, Database references