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- PDB-2kro: RDC refined high resolution structure of the third SH3 domain of CD2AP -

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Basic information

Entry
Database: PDB / ID: 2kro
TitleRDC refined high resolution structure of the third SH3 domain of CD2AP
ComponentsCD2-associated protein
KeywordsSIGNALING PROTEIN / protein / SH3 domain
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 / vascular endothelial growth factor receptor binding / negative regulation of transforming growth factor beta1 production / slit diaphragm ...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 / vascular endothelial growth factor receptor binding / negative regulation of transforming growth factor beta1 production / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / vesicle organization / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / cell-cell adhesion mediated by cadherin / collateral sprouting / protein heterooligomerization / renal albumin absorption / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / glomerulus development / cell-cell junction organization / filopodium assembly / podosome / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / cell leading edge / glucose import / filamentous actin / neurotrophin TRK receptor signaling pathway / centriolar satellite / protein secretion / endocytic vesicle / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / trans-Golgi network membrane / liver development / kidney development / cell periphery / positive regulation of protein secretion / actin filament / regulation of actin cytoskeleton organization / actin filament organization / synapse organization / protein catabolic process / response to virus / regulation of synaptic plasticity / response to insulin / neuromuscular junction / lipid metabolic process / fibrillar center / beta-catenin binding / cell-cell adhesion / response to wounding / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / neuron projection development / cell-cell junction / actin filament binding / protein transport / cell migration / late endosome / actin binding / T cell receptor signaling pathway / gene expression / cell cortex / growth cone / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / response to oxidative stress / negative regulation of neuron apoptotic process / cell population proliferation / cell differentiation / cadherin binding / inflammatory response / neuron projection / cell cycle / cell division / axon / apoptotic process / dendrite / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / cytosol
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 / Src homology 3 (SH3) domain profile. ...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
AuthorsOrtega Roldan, J. / Azuaga, A.I. / van Nuland, N.A.J. / Blackledge, M.
CitationJournal: To be Published
Title: Solution Structure, Dynamics and Thermodynamics of the three SH3 domains of CD2AP
Authors: Ortega Roldan, J.L. / Blackledge, M. / van Nuland, N.A.J. / Azuaga, A.I.
History
DepositionDec 21, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)10 / 200structures 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-C domain, UNP 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
1623D HNCO JNH
1723D HNCO JHNC
1823D HNCO JCC
1923D HN(CO)CA JCaHa

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] SH3-C, 90% H2O/10% D2O90% H2O/10% D2O
20.6-0.8 mM [U-98% 13C; U-98% 15N] SH3-C, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSH3-C[U-98% 13C; U-98% 15N]1
0.6 mMSH3-C[U-98% 13C; U-98% 15N]2
Sample conditionsIonic strength: 0 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SCULPTORHus, Marion and Blackledgerefinement
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: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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