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- PDB-9kon: Solid-state NMR Structure of VsSemiSWEET in Lipid Bilayers -

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Basic information

Entry
Database: PDB / ID: 9kon
TitleSolid-state NMR Structure of VsSemiSWEET in Lipid Bilayers
ComponentsSugar transporter SemiSWEET
KeywordsMEMBRANE PROTEIN / Transporter / Dimer / Sugar
Function / homologyidentical protein binding / membrane / plasma membrane / Sugar transporter SemiSWEET
Function and homology information
Biological speciesVibrio sp. (bacteria)
MethodSOLID-STATE NMR / molecular dynamics
AuthorsZhang, Y. / Yang, J.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22434003 China
National Natural Science Foundation of China (NSFC)21927801 China
Chinese Academy of SciencesYJKYYQ20190032 China
National Natural Science Foundation of China (NSFC)22004124 China
CitationJournal: To Be Published
Title: Diverse regulations of functional dimerization of a sugar transporter by different interfacial lipids
Authors: Zhang, Y. / Yang, J.
History
DepositionNov 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar transporter SemiSWEET
B: Sugar transporter SemiSWEET


Theoretical massNumber of molelcules
Total (without water)17,8852
Polymers17,8852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1024structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sugar transporter SemiSWEET


Mass: 8942.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. (strain N418) (bacteria) / Gene: VIBRN418_06191 / Production host: Escherichia coli (E. coli) / References: UniProt: F9RBV9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NCA
121isotropic12D DARR
131isotropic23D NCACX
141isotropic23D NCOCX
151isotropic23D CONCA
162isotropic12D CORD

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solid148 % w/w [U-13C; U-15N] VsSemiSWEET, 29 % w/w E.coli Lipids, 23 % w/w H2O, 100% H2O15N,13C_Sample100% H2O
solid248 % w/w [2-13C; U-15N] VsSemiSWEET, 29 % w/w E.coli lipids, 23 % w/w H2O, 100% H2O2-13C_Sample100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
48 % w/wVsSemiSWEET[U-13C; U-15N]1
29 % w/wE.coli Lipidsnatural abundance1
23 % w/wH2Onatural abundance1
48 % w/wVsSemiSWEET[2-13C; U-15N]2
29 % w/wE.coli lipidsnatural abundance2
23 % w/wH2Onatural abundance2
Sample conditionsIonic strength: 1 M / Label: conditions_1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKY2.6T. D. Goddard and D. G. Knellerchemical shift assignment
X-PLOR NIH2.47Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpin3.6Bruker Biospincollection
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1024 / Conformers submitted total number: 10

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