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- PDB-1xmw: CD3 EPSILON AND DELTA ECTODOMAIN FRAGMENT COMPLEX IN SINGLE-CHAIN... -

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Entry
Database: PDB / ID: 1xmw
TitleCD3 EPSILON AND DELTA ECTODOMAIN FRAGMENT COMPLEX IN SINGLE-CHAIN CONSTRUCT
ComponentsChimeric CD3 mouse Epsilon and sheep Delta Ectodomain Fragment Complex
KeywordsSIGNALING PROTEIN / BETA-SHEET / C1-SET IMMUNOGLOBULIN SUPERFAMILY / H-BONDED G STRAND PAIR / SINGLE-CHAIN
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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / smoothened signaling pathway / positive regulation of interleukin-4 production / dendrite development / immunological synapse / positive regulation of calcium-mediated signaling / T cell proliferation / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / cerebellum development / response to nutrient / calcium-mediated signaling / apoptotic signaling pathway / SH3 domain binding / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of type II interferon production / cell-cell junction / positive regulation of T cell activation / T cell receptor signaling pathway / cell body / adaptive immune response / dendritic spine / membrane => GO:0016020 / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / Golgi apparatus / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface glycoprotein CD3 delta chain / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / 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 ...T-cell surface glycoprotein CD3 delta chain / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Ovis aries (sheep)
MethodSOLUTION NMR / simulated annealing
AuthorsSun, Z.-Y.J. / Kim, S.T. / Kim, I.C. / Fahmy, A. / Reinherz, E.L. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Solution structure of the CD3epsilondelta ectodomain and comparison with CD3epsilongamma as a basis for modeling T cell receptor topology and signaling.
Authors: Sun, Z.Y. / Kim, S.T. / Kim, I.C. / Fahmy, A. / Reinherz, E.L. / Wagner, G.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Remark 999SEQUENCE CD3 EPSILON AND DELTA ECTODOMAIN FRAGMENT COMPLEX IN SINGLE-CHAIN CONSTRUCt with the ...SEQUENCE CD3 EPSILON AND DELTA ECTODOMAIN FRAGMENT COMPLEX IN SINGLE-CHAIN CONSTRUCt with the linker sequence GSADDAKKDA AKKDDAKKDD AKKDGSQTNK AK (residue 80-112)

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Assembly

Deposited unit
A: Chimeric CD3 mouse Epsilon and sheep Delta Ectodomain Fragment Complex


Theoretical massNumber of molelcules
Total (without water)19,9551
Polymers19,9551
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)15 / 20structures with the lowest energy
RepresentativeModel #1lowest energy,fewest violations,closest to the average

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Components

#1: Protein Chimeric CD3 mouse Epsilon and sheep Delta Ectodomain Fragment Complex


Mass: 19955.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Ovis aries / Genus: Mus, Ovis / Species: , / Strain: , / Gene: CD3E, CD3D / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P22646, UniProt: P18438

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HN(CA)CB
141HN(COCA)CB
151HNCO
161HN(CA)CO
17315N-NOESY
183TOCSY
19313C-NOESY
1103TOCSY
11122D NOESY
1122TOCSY
1133C(CO)NH
1143H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM, U-15N,13C,2D90% H2O/10% D2O
20.5mM unlabeled100% D2O
30.5mM, U-15N,13C90% H2O/10% D2O
Sample conditionsIonic strength: 17mM NaPO4, 50mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE7502

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Processing

NMR software
NameVersionDeveloperClassification
PROSA3.7Guntertprocessing
XEASY1.3.13Bartelsdata analysis
CYANA1.0.4Guntertrefinement
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy,fewest violations,closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 15

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