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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
TitleSolution NMR structure of the isolated NTE domain of BT1762-63 levan transporter
ComponentsTonB-dependent receptor
KeywordsPROTEIN TRANSPORT / Glycan import / Transporter / N-terminal Domain / Ig-like fold
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain ...CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
TonB-dependent receptor / SusC homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRath, P. / Mazur, A. / Hiller, S.
CitationJournal: 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
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TonB-dependent receptor


Theoretical massNumber of molelcules
Total (without water)9,9471
Polymers9,9471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7600 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TonB-dependent receptor


Mass: 9947.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: HMPREF2534_01945 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139KIX6, UniProt: Q8A6W3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMIsolated NTE domain of BT1762-63 levan transporterU-15N, 13C-NTE1
1 mMIsolated NTE domain of BT1762-63 levan transporter_2U-15N, 13C-NTE1
1 mMIsolated NTE domain of BT1762-63 levan transporter_3U-15N, 13C-NTE1
1 mMIsolated NTE domain of BT1762-63 levan transporter_4U-15N, 13C-NTE1
1 mMIsolated NTE domain of BT1762-63 levan transporter_5U-15N, 13C-NTE1
Sample conditionsIonic strength: 150 mM / Label: NTE_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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