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- PDB-1z3k: Structural Insight into the Binding Diversity between the Tyr-Pho... -

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Basic information

Entry
Database: PDB / ID: 1z3k
TitleStructural Insight into the Binding Diversity between the Tyr-Phosphorylated Human EphrinBs and Nck2 SH2 Domain
ComponentsCytoplasmic protein NCK2Cytoplasm
KeywordsStructural Genomics / Unknown Function / Nck2 / SH2 domain / Eph receptor-ephrin mediated signaling
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 / phosphotyrosine residue binding / T cell activation / Downstream signal transduction / actin filament organization / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / cell migration / signaling receptor complex adaptor activity / 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 / cytosol / cytoplasm
Similarity search - Function
Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / 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 / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytoplasmic protein NCK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsRan, X. / Song, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural insight into the binding diversity between the Tyr-phosphorylated human ephrinBs and Nck2 SH2 domain.
Authors: Ran, X. / Song, J.
History
DepositionMar 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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)11,4251
Polymers11,4251
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 / 100structures accepted by CNS program with the lowest energy
Representative

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Components

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


Mass: 11424.827 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O43639

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 0.5mM Nck2 SH2 domain U-15N,13C; 20mM phosphate buffer NA; 90% H2O, 10% D2O
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

RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures accepted by CNS program with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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