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- PDB-2krm: RDC refined solution structure of the first SH3 domain of CD2AP -

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Basic information

Entry
Database: PDB / ID: 2krm
TitleRDC refined solution structure of the first SH3 domain of CD2AP
ComponentsCD2-associated protein
KeywordsSIGNALING PROTEIN / protein / SH3 domain
Function / homology
Function and homology information


regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / vesicle organization / immunological synapse formation / protein heterooligomerization / podosome ...regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / vesicle organization / immunological synapse formation / protein heterooligomerization / podosome / cell leading edge / filamentous actin / centriolar satellite / endocytic vesicle / stress-activated MAPK cascade / ruffle / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kidney development / cell periphery / actin filament organization / actin filament / positive regulation of protein secretion / regulation of actin cytoskeleton organization / synapse organization / protein catabolic process / neuromuscular junction / fibrillar center / beta-catenin binding / cell-cell adhesion / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell-cell junction / cell migration / late endosome / actin binding / T cell receptor signaling pathway / gene expression / cell cortex / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / cadherin binding / inflammatory response / cell cycle / axon / cell division / apoptotic process / dendrite / protein-containing complex binding / 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 / 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.A.J. / Azuaga, A.I. / van Nuland, N.A.J.
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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)6,7651
Polymers6,7651
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)10 / 50structures 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: 6764.564 Da / Num. of mol.: 1 / Fragment: SH3-A domain, UNP residues 2-58
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 HBHA(CO)NH
1522D 1H-15N HSQC IPAP
1613D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] SH3-A, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 15N] SH3-A, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSH3-A[U-98% 13C; U-98% 15N]1
1 mMSH3-A[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: 0 / NOE intraresidue total count: 0 / NOE long range total count: 0 / NOE medium range total count: 0 / NOE sequential total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1

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