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- PDB-1u5s: NMR structure of the complex between Nck-2 SH3 domain and PINCH-1... -

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Basic information

Entry
Database: PDB / ID: 1u5s
TitleNMR structure of the complex between Nck-2 SH3 domain and PINCH-1 LIM4 domain
Components
  • Cytoplasmic protein NCK2Cytoplasm
  • PINCH protein
KeywordsMETAL BINDING PROTEIN / Protein-protein complex / beta barrel / beta sheet / zinc finger
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 / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of integrin-mediated signaling pathway / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / Cell-extracellular matrix interactions ...Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of integrin-mediated signaling pathway / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / Cell-extracellular matrix interactions / cytoskeletal anchor activity / vesicle membrane / cell-cell junction organization / signal complex assembly / Activation of RAC1 / positive regulation of cell-substrate adhesion / Nephrin family interactions / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / positive regulation of focal adhesion assembly / RHOU GTPase cycle / ephrin receptor signaling pathway / signaling adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / T cell activation / phosphotyrosine residue binding / Downstream signal transduction / actin filament organization / establishment of protein localization / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / positive regulation of GTPase activity / VEGFA-VEGFR2 Pathway / cell-cell adhesion / cell-cell junction / signaling receptor complex adaptor activity / cell migration / scaffold protein binding / positive regulation of canonical NF-kappaB signal transduction / postsynaptic density / negative regulation of cell population proliferation / focal adhesion / negative regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / : / : / Cytoplasmic protein NCK / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. ...Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / : / : / Cytoplasmic protein NCK / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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 / Ribbon / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Cytoplasmic protein NCK2 / LIM and senescent cell antigen-like-containing domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, rigid body, torsion angle dynamics
AuthorsVaynberg, J. / Fukuda, T. / Vinogradova, O. / Velyvis, A. / Ng, L. / Wu, C. / Qin, J.
CitationJournal: Mol.Cell / Year: 2005
Title: Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility.
Authors: Vaynberg, J. / Fukuda, T. / Chen, K. / Vinogradova, O. / Velyvis, A. / Tu, Y. / Ng, L. / Wu, C. / Qin, J.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
B: PINCH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7274
Polymers15,5962
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 50structures with the most reperesentative side chains orientations on the complex interface
RepresentativeModel #1closest to the average

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Components

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


Mass: 8063.068 Da / Num. of mol.: 1 / Fragment: third SH3 domain (residues 192-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK2 / Plasmid: pTYB11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43639
#2: Protein PINCH protein / Particularly interesting new Cys-His protein / LIM and senescent cell antigen-like domains 1


Mass: 7532.742 Da / Num. of mol.: 1 / Fragment: fourth LIM domain (residues 188-251)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1 / Plasmid: pGex-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48059
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 13C-separated NOESY
1313D 15N-separated NOESY
1423D 15N-separated NOESY
15115N/13C-edited 15N,13C-separated NOESY
16215N/13C-edited 15N,13C-separated NOESY
NMR detailsText: The structures of free form SH3 and LIM4 domains were determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM LIM4 of PINCH-1 U-15N,13C, 1.5mM SH3-3 of Nck-2 unlabeled, 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM SH3-3 of Nck-2 U-15N,13C, 2.5mM LIM4 of PINCH-1, 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
31.3mM SH3-3 of Nck-2 U-15N,13C, 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
41.7mM LIM4 of PINCH-1, U-15N,13C 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
NMRPipeDelagliodata analysis
X-PLOR3.1Brungerstructure solution
Xplor-NIHClorestructure solution
Xplor-NIHClorerefinement
RefinementMethod: simulated annealing, molecular dynamics, rigid body, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the most reperesentative side chains orientations on the complex interface
Conformers calculated total number: 50 / Conformers submitted total number: 18

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