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- PDB-1zsg: beta PIX-SH3 complexed with an atypical peptide from alpha-PAK -

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Basic information

Entry
Database: PDB / ID: 1zsg
Titlebeta PIX-SH3 complexed with an atypical peptide from alpha-PAK
Components
  • Rho guanine nucleotide exchange factor 7
  • Serine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / SH3-peptide complex
Function / homology
Function and homology information


negative regulation of microtubule nucleation / negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of lamellipodium morphogenesis / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / focal adhesion assembly / gamma-tubulin binding / positive regulation of fibroblast migration ...negative regulation of microtubule nucleation / negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of lamellipodium morphogenesis / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / focal adhesion assembly / gamma-tubulin binding / positive regulation of fibroblast migration / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of intracellular estrogen receptor signaling pathway / DSCAM interactions / RHOV GTPase cycle / Activation of RAC1 downstream of NMDARs / regulation of axonogenesis / branching morphogenesis of an epithelial tube / NRAGE signals death through JNK / Fc-gamma receptor signaling pathway involved in phagocytosis / mitotic spindle pole / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / RHOA GTPase cycle / intercalated disc / Smooth Muscle Contraction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / localization / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / collagen binding / CD209 (DC-SIGN) signaling / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / EGFR downregulation / MAPK6/MAPK4 signaling / wound healing / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / positive regulation of GTPase activity / G alpha (12/13) signalling events / cell-cell junction / cell migration / lamellipodium / positive regulation of peptidyl-serine phosphorylation / chromosome / nervous system development / cell cortex / actin cytoskeleton organization / postsynapse / nuclear membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / positive regulation of cell migration / intracellular signal transduction / chromatin remodeling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / axon / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / neuronal cell body / apoptotic process / DNA damage response / positive regulation of cell population proliferation
Similarity search - Function
Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain ...Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 1 / Rho guanine nucleotide exchange factor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simluated annealing with torsion angle dynamics, Cartesian dynamics cooling
AuthorsMott, H.R. / Nietlispach, D. / Evetts, K.A. / Owen, D.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Analysis of the SH3 Domain of beta-PIX and Its Interaction with alpha-p21 Activated Kinase (PAK)
Authors: Mott, H.R. / Nietlispach, D. / Evetts, K.A. / Owen, D.
History
DepositionMay 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 7
B: Serine/threonine-protein kinase PAK 1


Theoretical massNumber of molelcules
Total (without water)9,9232
Polymers9,9232
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)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix / COOL-1 / p85 / PIX-SH3


Mass: 7499.181 Da / Num. of mol.: 1 / Fragment: sequence database residues 179-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF7, COOL1, KIAA0142, P85SPR, PAK3BP, PIXB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q14155
#2: Protein/peptide Serine/threonine-protein kinase PAK 1 / p21-activated kinase 1 / PAK-1 / P65-PAK / Alpha-PAK / PAk peptide


Mass: 2423.721 Da / Num. of mol.: 1 / Fragment: sequence database residues 183-204 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q13153, EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
23213C,15N-filtered, 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 15N labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
21mM 15N,13C labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM Na2SO4 7.3 1 atm298 K
2100 mM Na2SO4 7.3 1 atm298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Azara2.7Boucherprocessing
ANSIG3.3Kraulisdata analysis
ARIA1.2Linge & Nilgesstructure solution
CNS1.1Brunger et alstructure solution
CNS1.1Brunger et alrefinement
RefinementMethod: simluated annealing with torsion angle dynamics, Cartesian dynamics cooling
Software ordinal: 1
Details: Total of 1788 unambiguous and 761 ambiguous NOE derieved distance restraints, 33 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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