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- PDB-2k4f: Mouse CD3epsilon Cytoplasmic Tail -

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Basic information

Entry
Database: PDB / ID: 2k4f
TitleMouse CD3epsilon Cytoplasmic Tail
ComponentsT-cell surface glycoprotein CD3 epsilon chain
KeywordsIMMUNE SYSTEM / signaling protein / ITAM / TCR / CD3E / Membrane bound protein / Bicelle / Immunoglobulin domain / Membrane / Phosphoprotein / Receptor / Transmembrane
Function / homology
Function and homology information


lymphocyte activation / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / Downstream TCR signaling / CD4-positive, alpha-beta T cell proliferation ...lymphocyte activation / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / Downstream TCR signaling / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of cell-matrix adhesion / T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / smoothened signaling pathway / dendrite development / immunological synapse / positive regulation of interleukin-4 production / negative regulation of smoothened signaling pathway / T cell proliferation / positive regulation of calcium-mediated signaling / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / cerebellum development / T cell activation / response to nutrient / calcium-mediated signaling / apoptotic signaling pathway / SH3 domain binding / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / positive regulation of type II interferon production / transmembrane signaling receptor activity / cell body / T cell receptor signaling pathway / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ig-like domain profile. / Immunoglobulin-like domain ...Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsMouse CD3epsilon cytoplasmic tail containing one ITAM domain
AuthorsXu, C. / Call, M.E. / Schwieters, C.D. / Schnell, J.R. / Gagnon, E.E. / Wucherpfennig, K.W. / Chou, J.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Regulation of T Cell Receptor Activation by Dynamic Membrane Binding of the CD3varepsilon Cytoplasmic Tyrosine-Based Motif.
Authors: Xu, C. / Gagnon, E. / Call, M.E. / Schnell, J.R. / Schwieters, C.D. / Carman, C.V. / Chou, J.J. / Wucherpfennig, K.W.
History
DepositionJun 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD3 epsilon chain


Theoretical massNumber of molelcules
Total (without water)6,3131
Polymers6,3131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein T-cell surface glycoprotein CD3 epsilon chain / T-cell surface antigen T3/Leu-4 epsilon chain


Mass: 6313.181 Da / Num. of mol.: 1 / Fragment: Cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd3e / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22646

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Mouse CD3epsilon cytoplasmic tail containing one ITAM domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1323D HNCA
1423D HN(CA)CB
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1713D 1H-13C NOESY (Methyl)
1813D 1H-13C NOESY aromatic
1923D 1H-15N NOESY (NOEs to lipid)
11013D 1H-13C NOESY (double 13C-filtered)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] Mouse CD3e, 100 mM POPG, 125 mM [U-100% 2H] DHPC, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 13C; U-100% 15N; 90% 2H] Mouse CD3e, 100 mM POPG, 125 mM [U-100% 2H] DHPC, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMMouse CD3e[U-100% 13C; U-100% 15N]1
100 mMPOPG1
125 mMDHPC[U-100% 2H]1
0.6 mMMouse CD3e[U-100% 13C; U-100% 15N; 90% 2H]2
100 mMPOPG2
125 mMDHPC[U-100% 2H]2
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
X-PLOR NIH2.19Schwieters, C.D. et al.structure solution
X-PLOR NIH2.19Schwieters, C.D. et al.refinement
NMRPipe3Delaglio, F. et al.processing
NMRPipe3Delaglio, F. et al.peak picking
XEASY1.2Bartels, C. et al.data analysis
XEASY1.2Bartels, C. et al.chemical shift assignment
XEASY1.2Bartels, C. et al.peak picking
RefinementMethod: simulated annealing, molecular dynamics / 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: 20

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