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- PDB-2frw: Solution structure of the second SH3 domain of human adaptor prot... -

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Basic information

Entry
Database: PDB / ID: 2frw
TitleSolution structure of the second SH3 domain of human adaptor protein NCK2
ComponentsCytoplasmic protein NCK2
KeywordsPROTEIN BINDING / SH3
Function / homology
Function and homology information


Regulation of cortical dendrite branching / regulation of translation initiation in response to endoplasmic reticulum stress / 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 / signal complex assembly / Activation of RAC1 / Nephrin family interactions ...Regulation of cortical dendrite branching / regulation of translation initiation in response to endoplasmic reticulum stress / 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 / signal complex assembly / Activation of RAC1 / Nephrin family interactions / vesicle membrane / 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 / phosphotyrosine residue binding / Downstream signal transduction / T cell activation / actin filament organization / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / cell migration / signaling receptor complex adaptor activity / scaffold protein binding / postsynaptic density / negative regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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 ...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 / SH2 domain / SH3 type barrels. / 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 / distance geometry, simulated annealing
AuthorsLiu, J.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Insight into the Binding Diversity between the Human Nck2 SH3 Domains and Proline-Rich Proteins
Authors: Liu, J. / Li, M. / Ran, X. / Fan, J.S. / Song, J.
History
DepositionJan 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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: Cytoplasmic protein NCK2


Theoretical massNumber of molelcules
Total (without water)6,5661
Polymers6,5661
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 / 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: 6566.346 Da / Num. of mol.: 1 / Fragment: SH3_2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32-a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O43639

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 50mM phosphate buffer, pH 6.8, 90% H2O, 10% D2O, 0.01% NaN3, DDT 10mM
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: A.T.Brunger / Classification: refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 974 restraints, 880 are NOE-derived distance constraints, 87 dihedral angle restraints,7 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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