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- PDB-1jbj: CD3 Epsilon and gamma Ectodomain Fragment Complex in Single-Chain... -

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Basic information

Entry
Database: PDB / ID: 1jbj
TitleCD3 Epsilon and gamma Ectodomain Fragment Complex in Single-Chain Construct
ComponentsCD3 Epsilon and gamma Ectodomain Fragment Complex
KeywordsIMMUNE SYSTEM / beta-sheet / C2-set IMMUNOGLOBULIN SUPERFAMILY / H-bonded G strand pair / single-chain
Function / homology
Function and homology information


lymphocyte activation / regulation of lymphocyte apoptotic process / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / FCGR activation / Role of phospholipids in phagocytosis / T cell anergy / positive regulation of T cell anergy ...lymphocyte activation / regulation of lymphocyte apoptotic process / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / FCGR activation / Role of phospholipids in phagocytosis / 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 / Regulation of actin dynamics for phagocytic cup formation / negative thymic T cell selection / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / T cell receptor complex / positive regulation of cell-matrix adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / smoothened signaling pathway / establishment or maintenance of cell polarity / dendrite development / immunological synapse / T cell differentiation / positive regulation of interleukin-4 production / negative regulation of smoothened signaling pathway / positive regulation of calcium-mediated signaling / T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / cerebellum development / T cell activation / response to nutrient / apoptotic signaling pathway / calcium-mediated signaling / SH3 domain binding / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / transmembrane signaling receptor activity / positive regulation of type II interferon production / protein transport / cell body / T cell receptor signaling pathway / dendritic spine / adaptive immune response / membrane => GO:0016020 / cell surface receptor signaling pathway / protein heterodimerization activity / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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 gamma chain / T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsSun, Z.-Y.J. / Kim, K.S. / Wagner, G. / Reinherz, E.L.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Mechanisms contributing to T cell receptor signaling and assembly revealed by the solution structure of an ectodomain fragment of the CD3 epsilon gamma heterodimer.
Authors: Sun, Z.J. / Kim, K.S. / Wagner, G. / Reinherz, E.L.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Heterodimeric CD3epsilongamma Extracellular Domain Fragments: Production, Purification and Structural Analysis
Authors: Kim, K.S. / Sun, Z.Y. / Wagner, G. / Reinherz, E.L.
History
DepositionJun 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD3 Epsilon and gamma Ectodomain Fragment Complex


Theoretical massNumber of molelcules
Total (without water)20,6331
Polymers20,6331
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)18 / 20structures with the least restraint violations
RepresentativeModel #12lowest energy

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Components

#1: Protein CD3 Epsilon and gamma Ectodomain Fragment Complex


Mass: 20632.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-79 ARE a fragment of T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN, RESIDUES 80-105 ARE AN ENGINEERED LINKER MODELED FROM A SINGLE CHAIN T CELL RECEPTOR CONSTRUCT, RESIDUES 106- ...Details: RESIDUES 1-79 ARE a fragment of T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN, RESIDUES 80-105 ARE AN ENGINEERED LINKER MODELED FROM A SINGLE CHAIN T CELL RECEPTOR CONSTRUCT, RESIDUES 106-186 ARE a fragment of T-CELL SURFACE GLYCOPROTEIN CD3 GAMMA CHAIN
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd3e FOR EPSILON CHAIN/CD3G FOR GAMMA CHAIN / Plasmid: pET-11a / Production host: Escherichia coli (E. coli)
References: UniProt: P22646, GenBank: 1531627, UniProt: P11942

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA,HN(CO)CA,HN(CA)CB,HN(COCA)CB,HNCO,HN(CA)CO
2222D-NOESY,2D-TOCSY
333H(CCO)NH
44415N-NOESYHSQC,TOCSY
55513C-NOESYHSQC,TOCSY
66613C-HSQC
47415N-HSQC,HNHA,HNHB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Structures are superimposed based on backbone atoms from residues 7 to 79 and 113 to 184.

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N,13C,2D; 5 mM sodium acetate, pH 4.590% H2O/10% D2O
2unlabeled; 5 mM sodium acetate, pH 4.5100% D2O
3U-15N,13C, U-70% 2D; 5 mM sodium acetate, pH 4.590% H2O/10% D2O
4U-15N; 5 mM sodium acetate, pH 4.590% H2O/10% D2O
5U-13C; 5 mM sodium acetate, pH 4.5100% D2O
6U-10% 13C; 5 mM sodium acetate, pH 4.5100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM sodium acetate 4.5 ambient 298 K
25 mM sodium acetate 4.5 ambient 298 K
35 mM sodium acetate 4.5 ambient 298 K
45 mM sodium acetate 4.5 ambient 298 K
55 mM sodium acetate 4.5 ambient 298 K
65 mM sodium acetate 4.5 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
PROSA3.7Guntertprocessing
XEASY1.3.13Bartelsdata analysis
DYANA1.4Guntertstructure solution
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: calculated using 1623 NOE restraints, 105 H-bond restraints, and 194 dihedral angle restrints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 18

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