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- PDB-2nae: Membrane-bound mouse CD28 cytoplasmic tail -

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Basic information

Entry
Database: PDB / ID: 2nae
TitleMembrane-bound mouse CD28 cytoplasmic tail
ComponentsT-cell-specific surface glycoprotein CD28
KeywordsSIGNALING PROTEIN / CD28 / membrane bound protein / bicelle / costimulation / TCR
Function / homology
Function and homology information


CD28 dependent PI3K/Akt signaling / CD28 dependent Vav1 pathway / CD28 co-stimulation / regulatory T cell differentiation / : / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / PIP3 activates AKT signaling / positive regulation of alpha-beta T cell proliferation ...CD28 dependent PI3K/Akt signaling / CD28 dependent Vav1 pathway / CD28 co-stimulation / regulatory T cell differentiation / : / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / PIP3 activates AKT signaling / positive regulation of alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / immune system process / positive regulation of interleukin-4 production / positive regulation of interleukin-10 production / immunological synapse / positive regulation of T cell proliferation / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / apoptotic signaling pathway / T cell receptor signaling pathway / protease binding / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / membrane raft / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsLi, H. / Xu, C. / Pan, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2017
Title: Dynamic regulation of CD28 conformation and signaling by charged lipids and ions.
Authors: Yang, W. / Pan, W. / Chen, S. / Trendel, N. / Jiang, S. / Xiao, F. / Xue, M. / Wu, W. / Peng, Z. / Li, X. / Ji, H. / Liu, X. / Jiang, H. / Wang, H. / Shen, H. / Dushek, O. / Li, H. / Xu, C.
History
DepositionDec 23, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 24, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: T-cell-specific surface glycoprotein CD28


Theoretical massNumber of molelcules
Total (without water)5,0941
Polymers5,0941
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)10 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide T-cell-specific surface glycoprotein CD28


Mass: 5093.790 Da / Num. of mol.: 1 / Fragment: UNP residues 177-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd28 / Production host: Escherichia coli (E. coli) / References: UniProt: P31041

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D 1H-15N NOESY (NOEs to lipid)
1413D 1H-13C NOESY (methyl; double 13C-filter)
1512D 1H-13C NOESY (aromatic; double 13C-filter)
1612D 1H-15N HSQC
1712D 1H-13C HSQC
1813D HNCO
1913D HNCA
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D C(CO)NH
11313D HBHA(CO)NH
11413D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] mCD28CD-1, 100 mM POPG-2, 125 mM DHPC-3, 20 mM sodium phosphate-4, 10 % [U-2H] D2O-5, 90 % H2O-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMmCD28CD-1[U-13C; U-15N]1
100 mMPOPG-21
125 mMDHPC-31
20 mMsodium phosphate-41
10 %D2O-5[U-2H]1
90 %H2O-61
Sample conditionsIonic strength: 20 / pH: 6.7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2Johnson, One Moon Scientificdata analysis
KUJIRA0.9843Naohiro Kobayashidata analysis
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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