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- PDB-2fei: Solution structure of the second SH3 domain of Human CMS protein -

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Basic information

Entry
Database: PDB / ID: 2fei
TitleSolution structure of the second SH3 domain of Human CMS protein
ComponentsCD2-associated protein
KeywordsSTRUCTURAL PROTEIN / CMS SH3 domain
Function / homology
Function and homology information


response to glial cell derived neurotrophic factor / 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 / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation ...response to glial cell derived neurotrophic factor / 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 / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / cell-cell adhesion mediated by cadherin / collateral sprouting / protein heterooligomerization / renal albumin absorption / substrate-dependent cell migration, cell extension / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / cell-cell junction organization / filopodium assembly / podosome / Nephrin family interactions / 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 / 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 / positive regulation of protein secretion / 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 / structural constituent of cytoskeleton / fibrillar center / response to wounding / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / actin filament binding / cell migration / actin cytoskeleton / late endosome / T cell receptor signaling pathway / growth cone / protein-containing complex assembly / vesicle / response to oxidative stress / negative regulation of neuron apoptotic process / cell population proliferation / cadherin binding / inflammatory response / cell cycle / cell division / axon / apoptotic process / dendrite / signal transduction / extracellular exosome / identical protein binding / plasma membrane / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics torsion angle dynamics
AuthorsYao, B. / Dai, H. / Jiao, Y. / Wu, J. / Shi, Y.
CitationJournal: Biochim.Biophys.Acta / Year: 2007
Title: Solution structure of the second SH3 domain of human CMS and a newly identified binding site at the C-terminus of c-Cbl
Authors: Yao, B. / Zhang, J. / Dai, H. / Sun, J. / Jiao, Y. / Tang, Y. / Wu, J. / Shi, Y.
History
DepositionDec 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4May 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)7,7771
Polymers7,7771
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein CD2-associated protein / Cas ligand with multiple SH3 domains / Adapter protein CMS


Mass: 7776.661 Da / Num. of mol.: 1 / Fragment: The second SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMS / Plasmid: PET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5K6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-2.0mM 15N, 13C-labeled CMS SH3 domain, 20mM phosphate buffer (pH 6.85), 50mM sodium chloride, 90% H2O, 10% D2O90% H2O/10% D2O
21.0-2.0mM 15N, 13C-labeled CMS SH3 domain, 20mM phosphate buffer (pH 6.85), 50mM sodium chloride, 100% D2O100% D2O
Sample conditionspH: 6.85 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
CNS1.1A.T.Brungerstructure solution
Sparky3T.D.Goddard and D.G.Knellerdata analysis
MOLMOL2K.2Koradidata analysis
CNS1.1A.T.Brungerrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: The solution structure is solved using a total of 1,112 experimental restraints that includes 1,036 distance restraints, 70 dihedral angles restraints and 12 hydrogen bonds restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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