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- PDB-2df6: Crystal Structure of the SH3 Domain of betaPIX in Complex with a ... -

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Basic information

Entry
Database: PDB / ID: 2df6
TitleCrystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2
Components
  • 18-mer from PAK2
  • Rho guanine nucleotide exchange factor 7
KeywordsSIGNALING PROTEIN / SH3 domain / Peptide interaction
Function / homology
Function and homology information


CD28 dependent Vav1 pathway / negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / CD209 (DC-SIGN) signaling / signal transduction => GO:0007165 / presynaptic actin cytoskeleton organization / VEGFA-VEGFR2 Pathway / small GTPase binding => GO:0031267 ...CD28 dependent Vav1 pathway / negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / CD209 (DC-SIGN) signaling / signal transduction => GO:0007165 / presynaptic actin cytoskeleton organization / VEGFA-VEGFR2 Pathway / small GTPase binding => GO:0031267 / negative regulation of microtubule nucleation / Generation of second messenger molecules / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / Smooth Muscle Contraction / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RHOQ GTPase cycle / RAC1 GTPase cycle / RHOA GTPase cycle / FCERI mediated MAPK activation / protein localization to cell-cell junction / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / dendritic spine development / bicellular tight junction assembly / adherens junction assembly / gamma-tubulin binding / cardiac muscle hypertrophy / positive regulation of extrinsic apoptotic signaling pathway / lamellipodium assembly / negative regulation of stress fiber assembly / regulation of cytoskeleton organization / small GTPase-mediated signal transduction / regulation of axonogenesis / stress-activated protein kinase signaling cascade / protein tyrosine kinase activator activity / mitotic spindle pole / Golgi organization / activation of protein kinase activity / Rho protein signal transduction / cellular response to organic cyclic compound / GABA-ergic synapse / hematopoietic progenitor cell differentiation / ruffle / cellular response to transforming growth factor beta stimulus / guanyl-nucleotide exchange factor activity / secretory granule / small GTPase binding / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / lamellipodium / cell cortex / growth cone / postsynapse / peptidyl-serine phosphorylation / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / positive regulation of apoptotic process / phosphorylation / protein phosphorylation / focal adhesion / centrosome / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21-activated kinase 2, catalytic domain / Serine/threonine-protein kinase PAK2 / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / 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 ...p21-activated kinase 2, catalytic domain / Serine/threonine-protein kinase PAK2 / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / 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 / 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
: / Rho guanine nucleotide exchange factor 7 / Serine/threonine-protein kinase PAK 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2
Authors: Hoelz, A. / Janz, J.M. / Lawrie, S.D. / Corwin, B. / Lee, A. / Sakmar, T.P.
History
DepositionFeb 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
C: 18-mer from PAK2
D: 18-mer from PAK2


Theoretical massNumber of molelcules
Total (without water)17,5694
Polymers17,5694
Non-polymers00
Water2,540141
1
A: Rho guanine nucleotide exchange factor 7
C: 18-mer from PAK2


Theoretical massNumber of molelcules
Total (without water)8,7852
Polymers8,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4 kcal/mol
Surface area4530 Å2
MethodPISA
2
B: Rho guanine nucleotide exchange factor 7
D: 18-mer from PAK2


Theoretical massNumber of molelcules
Total (without water)8,7852
Polymers8,7852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.217, 50.217, 100.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 6731.333 Da / Num. of mol.: 2 / Fragment: SH3 domain(residues 10-63)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef7, Pak3bp, Pixb / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O55043
#2: Protein/peptide 18-mer from PAK2


Mass: 2053.364 Da / Num. of mol.: 2 / Fragment: residues 180-197 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human, rat.
References: GenBank: 5138914, UniProt: Q64303*PLUS, EC: 2.7.1.37
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100mM MES, 35% PEG 5000MME, 200mM ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979191 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 35167 / Num. obs: 35167 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.32 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G6F

2g6f


Resolution: 1.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.215 3343
Rwork0.201 -
all0.204 35167
obs0.204 35167
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 0 141 1336

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