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- PDB-2jte: Third SH3 domain of CD2AP -

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Basic information

Entry
Database: PDB / ID: 2jte
TitleThird SH3 domain of CD2AP
ComponentsCD2-associated protein
KeywordsSIGNALING PROTEIN / protein / SH3 domain / Coiled coil / Cytoplasm / Phosphorylation / SH3-binding
Function / homology
Function and homology information


neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / response to transforming growth factor beta ...neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / response to transforming growth factor beta / slit diaphragm / vesicle organization / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / collateral sprouting / protein heterooligomerization / cell-cell adhesion mediated by cadherin / renal albumin absorption / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / glomerulus development / filopodium assembly / cell-cell junction organization / podosome / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / D-glucose import / cell leading edge / filamentous actin / neurotrophin TRK receptor signaling pathway / endocytic vesicle / centriolar satellite / protein secretion / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / actin filament polymerization / ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / liver development / trans-Golgi network membrane / actin filament organization / kidney development / cell periphery / actin filament / positive regulation of protein secretion / regulation of actin cytoskeleton organization / response to insulin / synapse organization / response to virus / neuromuscular junction / protein catabolic process / regulation of synaptic plasticity / lipid metabolic process / fibrillar center / response to wounding / cell-cell adhesion / positive regulation of protein localization to nucleus / SH3 domain binding / beta-catenin binding / male gonad development / actin filament binding / neuron projection development / cell-cell junction / cell migration / protein transport / late endosome / T cell receptor signaling pathway / actin binding / gene expression / cell cortex / growth cone / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / negative regulation of neuron apoptotic process / response to oxidative stress / cell population proliferation / cell differentiation / neuron projection / cadherin binding / inflammatory response / axon / cell division / dendrite / protein-containing complex binding / apoptotic process / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily ...CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
CD2-associated protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Authorsvan Nuland, N.A.J. / Ortega, R.J. / Romero Romero, M. / Ab, E. / Ora, A. / Lopez, M.O. / Azuaga, A.I.
CitationJournal: J.Biomol.Nmr / Year: 2007
Title: The high resolution NMR structure of the third SH3 domain of CD2AP.
Authors: Ortega Roldan, J.L. / Romero Romero, M.L. / Ora, A. / Ab, E. / Lopez Mayorga, O. / Azuaga, A.I. / van Nuland, N.A.
History
DepositionJul 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CD2-associated protein


Theoretical massNumber of molelcules
Total (without water)7,1471
Polymers7,1471
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 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CD2-associated protein / Mesenchyme-to-epithelium transition protein with SH3 domains 1 / METS-1


Mass: 7146.910 Da / Num. of mol.: 1 / Fragment: SH3 domain, residues 270-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd2ap, Mets1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JLQ0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11022D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM SH3-C, 1 mM [U-98% 15N] SH3-C, 1 mM [U-98% 13C; U-98% 15N] SH3-C, 90% H2O/10% D2O90% H2O/10% D2O
21 mM SH3-C, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSH3-C-11
1 mMSH3-C-2[U-98% 15N]1
1 mMSH3-C-3[U-98% 13C; U-98% 15N]1
1 mMSH3-C2
Sample conditionsIonic strength: 100 / pH: 2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1041 / NOE intraresidue total count: 241 / NOE long range total count: 394 / NOE medium range total count: 109 / NOE sequential total count: 297
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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