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- PDB-2jxb: Structure of CD3epsilon-Nck2 first SH3 domain complex -

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Basic information

Entry
Database: PDB / ID: 2jxb
TitleStructure of CD3epsilon-Nck2 first SH3 domain complex
ComponentsT-cell surface glycoprotein CD3 epsilon chain, Cytoplasmic protein NCK2
KeywordsSignaling protein complex / Nck / CD3epsilon / T-cell receptor / SH3 domain / Immunology / Cytoplasm / SH2 domain
Function / homology
Function and homology information


Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / gamma-delta T cell receptor complex / positive regulation of translation in response to endoplasmic reticulum stress / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation ...Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / gamma-delta T cell receptor complex / positive regulation of translation in response to endoplasmic reticulum stress / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / dendritic spine development / cytoskeletal anchor activity / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / vesicle membrane / positive thymic T cell selection / signal complex assembly / Activation of RAC1 / Nephrin family interactions / Ephrin signaling / positive regulation of cell-matrix adhesion / lamellipodium assembly / T cell receptor complex / smoothened signaling pathway / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / positive regulation of interleukin-4 production / dendrite development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / RHOU GTPase cycle / Generation of second messenger molecules / immunological synapse / PD-1 signaling / ephrin receptor signaling pathway / T cell receptor binding / positive regulation of calcium-mediated signaling / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / phosphotyrosine residue binding / Downstream signal transduction / cerebellum development / calcium-mediated signaling / apoptotic signaling pathway / actin filament organization / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / cell-cell junction / signaling receptor complex adaptor activity / cell migration / Downstream TCR signaling / T cell receptor signaling pathway / cell body / scaffold protein binding / protein-containing complex assembly / regulation of apoptotic process / adaptive immune response / dendritic spine / postsynaptic density / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / external side of plasma membrane / negative regulation of gene expression / protein-containing complex binding / positive regulation of gene expression / protein kinase binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / 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. ...Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / 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 / Variant SH3 domain / SH3 Domains / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Cytoplasmic protein NCK2 / T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsTakeuchi, K. / Yang, H. / Ng, E. / Park, S. / Sun, Z.J. / Reinherz, E.L. / Wagner, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural and functional evidence that Nck interaction with CD3epsilon regulates T-cell receptor activity.
Authors: Takeuchi, K. / Yang, H. / Ng, E. / Park, S.Y. / Sun, Z.Y. / Reinherz, E.L. / Wagner, G.
History
DepositionNov 9, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 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_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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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, Cytoplasmic protein NCK2


Theoretical massNumber of molelcules
Total (without water)10,2681
Polymers10,2681
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein T-cell surface glycoprotein CD3 epsilon chain, Cytoplasmic protein NCK2 / T-cell surface antigen T3/Leu-4 epsilon chain / NCK adaptor protein 2 / SH2/SH3 adaptor protein NCK- ...T-cell surface antigen T3/Leu-4 epsilon chain / NCK adaptor protein 2 / SH2/SH3 adaptor protein NCK-beta / Nck-2


Mass: 10267.655 Da / Num. of mol.: 1
Fragment: Fusion protein of T-cell surface glycoprotein CD3 epsilon chain cytoplasmic domain residues 177-188 and Cytoplasmic protein NCK2 first SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3E, NCK2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: O43639, UniProt: P07766

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CA)CB
1313D HN(CO)CA
1413D H(CCO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY

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Sample preparation

DetailsContents: 2 mM [U-13C; U-15N] entity, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: entity / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
XwinNMRBruker Biospincollection
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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