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- PDB-2rol: Structural Basis of PxxDY motif recognition in SH3 binding -

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Basic information

Entry
Database: PDB / ID: 2rol
TitleStructural Basis of PxxDY motif recognition in SH3 binding
Components
  • 12-meric peptide from T-cell surface glycoprotein CD3 epsilon chain
  • Epidermal growth factor receptor kinase substrate 8-like protein 1
KeywordsSPLICING/SIGNALING PROTEIN / EPS8L1 / CD3e / SH3 / Complex Structure / Alternative splicing / Coiled coil / Cytoplasm / SH3 domain / Immunoglobulin domain / Membrane / Phosphoprotein / Receptor / Transmembrane / SPLICING-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


gamma-delta T cell receptor complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / regulation of Rho protein signal transduction ...gamma-delta T cell receptor complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / regulation of Rho protein signal transduction / positive thymic T cell selection / signal complex assembly / positive regulation of ruffle assembly / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / dendrite development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Rho protein signal transduction / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / PD-1 signaling / positive regulation of interleukin-4 production / negative regulation of smoothened signaling pathway / 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 receptor binding / T cell activation / calcium-mediated signaling / apoptotic signaling pathway / ruffle membrane / SH3 domain binding / cell surface receptor protein tyrosine kinase signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / transmembrane signaling receptor activity / signaling receptor complex adaptor activity / positive regulation of type II interferon production / Downstream TCR signaling / cell body / actin binding / T cell receptor signaling pathway / protein-containing complex assembly / regulation of apoptotic process / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / cadherin binding / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / SAM domain (Sterile alpha motif) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif ...Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / SAM domain (Sterile alpha motif) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding 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 / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH3 Domains / Sterile alpha motif/pointed domain superfamily / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain / Epidermal growth factor receptor kinase substrate 8-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAitio, O. / Hellman, M. / Kesti, T. / Kleino, I. / Samuilova, O. / Tossavainen, H. / Paakkonen, K. / Saksela, K. / Permi, P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis of PxxDY motif recognition in SH3 binding
Authors: Aitio, O. / Hellman, M. / Kesti, T. / Kleino, I. / Samuilova, O. / Paakkonen, K. / Tossavainen, H. / Saksela, K. / Permi, P.
History
DepositionApr 2, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor kinase substrate 8-like protein 1
B: 12-meric peptide from T-cell surface glycoprotein CD3 epsilon chain


Theoretical massNumber of molelcules
Total (without water)8,6962
Polymers8,6962
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Epidermal growth factor receptor kinase substrate 8-like protein 1 / Epidermal growth factor receptor pathway substrate 8-related protein 1 / EPS8-like protein 1


Mass: 7301.153 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPS8L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TE68
#2: Protein/peptide 12-meric peptide from T-cell surface glycoprotein CD3 epsilon chain / T-cell surface antigen T3/Leu-4 epsilon chain


Mass: 1394.550 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic construct; this sequence occurs naturally in humans.
References: UniProt: P07766

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D iHNCACB
1813D iHNCA
1913D (H)CCH-COSY
11013D CC(CO)NH
11113D H(CCO)NH
11212D (HB)CB(CGCD)HD
11312D (HB)CB(CGCDCE)HE
11413D 1H-15N NOESY
11513D 1H-13C NOESY
11613D 1H-15N NOESY filteded/edited
11713D 1H-13C NOESY filtered/edited

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Sample preparation

DetailsContents: 0.8mM [U-98% 13C; U-98% 15N] Eps8L1SH3; 2.4mM CD3e peptide; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMEps8L1SH3[U-98% 13C; U-98% 15N]1
2.4 mMCD3e peptide1
Sample conditionspH: 7.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
VNMRVariancollection
VNMRVarianprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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