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- PDB-2lma: Solution structure of CD4+ T cell derived peptide Thp5 -

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Basic information

Entry
Database: PDB / ID: 2lma
TitleSolution structure of CD4+ T cell derived peptide Thp5
ComponentsThp5 peptide
KeywordsIMMUNE SYSTEM / Thp5 / CD4+
MethodSOLUTION NMR / distance geometry
Model detailsclosest to the average, model 1
AuthorsPandey, N.K. / Khan, M.M. / Chatterjee, S. / Dwivedi, V.P. / Tousif, S. / Das, J. / Van Kaer, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: CD4+ T cell derived novel peptide Thp5 induces IL-4 production in CD4+ T cells to direct T helper 2 cell differentiation
Authors: Khan, M.M. / Chatterjee, S. / Dwivedi, V.P. / Pandey, N.K. / Singh, Y. / Tousif, S. / Bhavesh, N.S. / Van Kaer, L. / Das, J. / Das, G.
History
DepositionNov 29, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 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: Thp5 peptide


Theoretical massNumber of molelcules
Total (without water)2,6931
Polymers2,6931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Thp5 peptide


Mass: 2693.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CD4+ T cell derived novel peptide

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of CD4+ T cell derived peptide Thp5
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-15N HSQC
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM protein-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein-1
Sample conditionsIonic strength: 200 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 40 / Representative conformer: 1

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