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- PDB-2b86: Solution structure of the first Src homology 3 domain of Nck2 -

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Basic information

Entry
Database: PDB / ID: 2b86
TitleSolution structure of the first Src homology 3 domain of Nck2
ComponentsCytoplasmic protein NCK2
KeywordsSIGNALING PROTEIN / Nck SH3 domain
Function / homology
Function and homology information


Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / cytoskeletal anchor activity / vesicle membrane / signal complex assembly ...Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / cytoskeletal anchor activity / vesicle membrane / signal complex assembly / Activation of RAC1 / Nephrin family interactions / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / RHOU GTPase cycle / ephrin receptor signaling pathway / signaling adaptor activity / positive regulation of T cell proliferation / T cell activation / phosphotyrosine residue binding / Downstream signal transduction / actin filament organization / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / signaling receptor complex adaptor activity / cell migration / scaffold protein binding / postsynaptic density / negative regulation of cell population proliferation / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / cytoplasm / cytosol
Similarity search - Function
Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. ...Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Cytoplasmic protein NCK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing tortion angle dynamics
AuthorsPark, S. / Takeuchi, K. / Wagner, G.
CitationJournal: J.BIOMOL.NMR / Year: 2006
Title: Solution structure of the first SRC homology 3 domain of human nck2
Authors: Park, S. / Takeuchi, K. / Wagner, G.
History
DepositionOct 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 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: 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 1.4May 22, 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: Cytoplasmic protein NCK2


Theoretical massNumber of molelcules
Total (without water)8,2531
Polymers8,2531
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytoplasmic protein NCK2 / NCK adaptor protein 2 / SH2/SH3 adaptor protein NCK-beta / Nck-2


Mass: 8253.205 Da / Num. of mol.: 1 / Fragment: First SH3 domain, residues 1-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK2 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O43639

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
NMR detailsText: cryogenic probes

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Sample preparation

DetailsContents: 600uM Nck SH3 domain U-15N, 13C, 50mM Sodium Phosphate, 50mM EDTA, pH 6.5, 5% D2O, 95% H2O
Solvent system: 5% D2O, 95% H2O
Sample conditionsIonic strength: 50mM phosphate / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
NMRPipe2.3Delaglioprocessing
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing tortion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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