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- PDB-2cub: Solution structure of the SH3 domain of the human cytoplasmic pro... -

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Basic information

Entry
Database: PDB / ID: 2cub
TitleSolution structure of the SH3 domain of the human cytoplasmic protein Nck1
ComponentsCytoplasmic protein NCK1
KeywordsSIGNALING PROTEIN / SH3 domain / NCK1 adaptor / tyrosine kinase / signal transduction / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / 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 / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension ...positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / : / eukaryotic initiation factor eIF2 binding / 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 / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / vesicle membrane / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / protein kinase inhibitor activity / negative regulation of peptidyl-serine phosphorylation / RHOU GTPase cycle / Generation of second messenger molecules / ephrin receptor signaling pathway / RHO GTPases Activate WASPs and WAVEs / signaling adaptor activity / positive regulation of T cell proliferation / antiviral innate immune response / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / regulation of cell migration / response to endoplasmic reticulum stress / Downstream signal transduction / T cell activation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / FCGR3A-mediated phagocytosis / molecular condensate scaffold activity / PKR-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / cell-cell junction / cell migration / 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 / 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 / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, 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
SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / tortion angle dynamics, restrained molecular dynamics
AuthorsOhnishi, S. / Kigawa, T. / Sato, M. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SH3 domain of the human cytoplasmic protein Nck1
Authors: Ohnishi, S. / Kigawa, T. / Sato, M. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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)9,5491
Polymers9,5491
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 9549.387 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: NCK1 / Plasmid: P040621-03 / References: UniProt: P16333

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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

DetailsContents: 1.18mM protein U-15N,13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / 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 software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: tortion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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