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- PDB-2jw4: NMR solution structure of the N-terminal SH3 domain of human Nckalpha -

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Basic information

Entry
Database: PDB / ID: 2jw4
TitleNMR solution structure of the N-terminal SH3 domain of human Nckalpha
ComponentsCytoplasmic protein NCK1Cytoplasm
KeywordsSIGNALING PROTEIN / SH3 domain / Cytoplasm / Phosphorylation / SH2 domain
Function / homology
Function and homology information


positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity ...positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / vesicle membrane / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / protein kinase inhibitor activity / antiviral innate immune response / RHOU GTPase cycle / Generation of second messenger molecules / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / signaling adaptor activity / negative regulation of peptidyl-serine phosphorylation / regulation of cell migration / negative regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / response to endoplasmic reticulum stress / ephrin receptor binding / T cell activation / Downstream signal transduction / molecular condensate scaffold activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / FCGR3A-mediated phagocytosis / PKR-mediated signaling / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / positive regulation of neuron projection development / VEGFA-VEGFR2 Pathway / cell migration / cell-cell junction / signaling receptor complex adaptor activity / protein-macromolecule adaptor activity / Potential therapeutics for SARS / ribosome / cadherin binding / protein domain specific binding / signaling receptor binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / 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
SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSantiveri, C.M. / Borroto, A. / Simon, L. / Rico, M. / Ortiz, A.R. / Alarcon, B. / Jimenez, M.
CitationJournal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2009
Title: Interaction between the N-terminal SH3 domain of Nckalpha and CD3epsilon-derived peptides: Non-canonical and canonical recognition motifs
Authors: Santiveri, C.M. / Borroto, A. / Simon, L. / Rico, M. / Alarcon, B. / Jimenez, M.A.
History
DepositionOct 5, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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 NCK1


Theoretical massNumber of molelcules
Total (without water)8,2911
Polymers8,2911
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)20 / 100target function
RepresentativeModel #1secondary structure criteria

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Components

#1: Protein Cytoplasmic protein NCK1 / Cytoplasm / NCK adaptor protein 1 / SH2/SH3 adaptor protein NCK-alpha


Mass: 8291.243 Da / Num. of mol.: 1 / Fragment: SH3 1 domain, sequence database residues 1-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK1, NCK / Production host: Escherichia coli (E. coli) / References: UniProt: P16333

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H NOESY
1532D 1H-15N HSQC
1633D 1H-15N NOESY
1742D 1H-15N HSQC
1843D HNCO
1943D HNCA
11043D CBCA(CO)NH
11143D CBCANH
11243D HBHA(CO)NH
11343D HACANH
11452D 1H-13C HSQC
11553D 1H-13C NOESY
11653D (H)CCH-TOCSY
11753D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Nckalpha-SH3.1, 50 mM sodium phosphate, 90 % H2O, 10 % [U-100% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM Nckalpha-SH3.1,, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 0.1 mM DSS, 100% D2O100% D2O
31 mM [U-100% 15N] Nckalpha-SH3.1, 50 mM sodium phosphate, 90 % H2O, 10 % [U-100% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
41.2 mM [U-100% 13C; U-100% 15N] Nckalpha-SH3.1, 50 mM sodium phosphate, 90 % H2O, 10 % [U-100% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
51.2 mM [U-100% 13C; U-100% 15N] Nckalpha-SH3.1, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 0.1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNckalpha-SH3.11
50 mMsodium phosphate1
90 %H2O1
10 %D2O[U-100% 2H]1
0.1 mMDSS1
1 mMNckalpha-SH3.1,2
50 mMsodium phosphate2
100 %D2O[U-100% 2H]2
0.1 mMDSS2
1 mMNckalpha-SH3.1[U-100% 15N]3
50 mMsodium phosphate3
90 %H2O3
10 %D2O[U-100% 2H]3
0.1 mMDSS3
1.2 mMNckalpha-SH3.1[U-100% 13C; U-100% 15N]4
50 mMsodium phosphate4
90 %H2O4
10 %D2O[U-100% 2H]4
0.1 mMDSS4
1.2 mMNckalpha-SH3.1[U-100% 13C; U-100% 15N]5
50 mMsodium phosphate5
100 %D2O[U-100% 2H]5
0.1 mMDSS5
Sample conditionsIonic strength: 0.05 / pH: 5.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
ProcheckNMRLaskowski and MacArthurstructure analysis
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
PROMOTIF(PROMOTIF)-Hutchinson and Thorntonstructure analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: secondary structure criteria
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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