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- PDB-1ees: SOLUTION STRUCTURE OF CDC42HS COMPLEXED WITH A PEPTIDE DERIVED FR... -

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Basic information

Entry
Database: PDB / ID: 1ees
TitleSOLUTION STRUCTURE OF CDC42HS COMPLEXED WITH A PEPTIDE DERIVED FROM P-21 ACTIVATED KINASE, NMR, 20 STRUCTURES
Components
  • GTP-BINDING PROTEING protein
  • P21-ACTIVATED KINASE
KeywordsSTRUCTURAL PROTEIN / protein-protein complex
Function / homology
Function and homology information


CD28 dependent Vav1 pathway / Ephrin signaling / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / GBD domain binding / submandibular salivary gland formation / actin filament branching / Generation of second messenger molecules / Golgi transport complex / protein serine/threonine kinase activity => GO:0004674 ...CD28 dependent Vav1 pathway / Ephrin signaling / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / GBD domain binding / submandibular salivary gland formation / actin filament branching / Generation of second messenger molecules / Golgi transport complex / protein serine/threonine kinase activity => GO:0004674 / VEGFR2 mediated vascular permeability / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / MAPK6/MAPK4 signaling / Inactivation of CDC42 and RAC1 / positive regulation of dendritic spine morphogenesis / cardiac conduction system development / dendritic spine development / CD209 (DC-SIGN) signaling / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / regulation of actin filament polymerization / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of fibroblast migration / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / positive regulation of DNA biosynthetic process / phagocytosis, engulfment / RHOV GTPase cycle / regulation of axonogenesis / stress-activated protein kinase signaling cascade / heart contraction / regulation of neuron projection development / Myogenesis / dendrite development / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / activation of protein kinase activity / RHO GTPases activate PAKs / MAP kinase kinase activity / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / cellular response to organic cyclic compound / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / positive regulation of DNA replication / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / small monomeric GTPase
Similarity search - Function
p21-activated kinase 3, catalytic domain / SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Cdc42 / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain ...p21-activated kinase 3, catalytic domain / SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Cdc42 / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog / Serine/threonine-protein kinase PAK 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / distance geometry simulated annealing Ramachandran refinement
AuthorsGizachew, D. / Guo, W. / Chohan, K.C. / Sutcliffe, M.J. / Oswald, R.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure of the complex of Cdc42Hs with a peptide derived from P-21 activated kinase.
Authors: Gizachew, D. / Guo, W. / Chohan, K.K. / Sutcliffe, M.J. / Oswald, R.E.
#1: Journal: Biochemistry / Year: 1999
Title: Backbone Dynamics of Inactive, Active, and Effector-Bound Cdc42Hs from Measurements of (15)N Relaxation Parameters at Multiple Field Strengths
Authors: Loh, A.P. / Guo, W. / Nicholson, L.K. / Oswald, R.E.
#2: Journal: Biochemistry / Year: 1998
Title: Identification of the Binding Surface on Cdc42Hs for p21-Activated Kinase
Authors: Guo, W. / Sutcliffe, M.J. / Cerione, R.A. / Oswald, R.E.
#3: Journal: Biochemistry / Year: 1997
Title: Definition of the Switch Surface in the Solution Structure of Cdc42Hs
Authors: Feltham, J.L. / Dotsch, V. / Raza, S. / Manor, D. / Cerione, R.A. / Sutcliffe, M.J. / Wagner, G. / Oswald, R.E.
History
DepositionFeb 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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

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Assembly

Deposited unit
A: GTP-BINDING PROTEIN
B: P21-ACTIVATED KINASE


Theoretical massNumber of molelcules
Total (without water)24,8922
Polymers24,8922
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 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #9closest to the average

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Components

#1: Protein GTP-BINDING PROTEIN / G protein / CDC42HS


Mass: 19774.705 Da / Num. of mol.: 1 / Fragment: AMINO ACIDS 1-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PLACENTA / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#2: Protein/peptide P21-ACTIVATED KINASE / MPAK-3


Mass: 5117.615 Da / Num. of mol.: 1 / Fragment: AMINO ACIDS 65-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: FIBROBLAST / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q61036

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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 15N-separated NOESY
1333D 13C-separated NOESY
1443D 15N-separated NOESY
1563D 15N-separated NOESY
1673D 13C-separated NOESY
1783D 13C-separated NOESY
1862D NOESY
NMR detailsText: The structure was determined using triple-resonance and double-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM U-15N,13C Cdc42Hs, 0.8 mM PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.590% H2O/10% D2O
20.8 mM U-15N Cdc42Hs, 0.8 mM PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.590% H2O/10% D2O
30.8 mM Cdc42Hs, 0.8 mM U-15N,13C PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.590% H2O/10% D2O
40.8 mM Cdc42Hs, 0.8 mM U-15N PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.590% H2O/10% D2O
50.8 mM 70%-2H,U-15N,13C Cdc42Hs, 0.8 mM PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.590% H2O/10% D2O
60.8 mM U-2H,15N Cdc42Hs, 0.8 mM PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.590% H2O/10% D2O
70.8 mM U-15N,13C Cdc42Hs, 0.8 mM PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.5100% D2O
80.8 mM Cdc42Hs, 0.8 mM U-15N,13C PBD46; 25 mM NaCl, 5 mM Na2PO4, 5 mM MgCl2, 1 mM NaN3, pH 5.5100% D2O
Sample conditionsIonic strength: 64 mM / pH: 5.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3,6.1Variancollection
Felix2.3Molecular Simulationsdata analysis
NMRPipe1.7Delaglioprocessing
XEASY1.3.13Wuthrichdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry simulated annealing Ramachandran refinement
Software ordinal: 1
Details: Structures are based on 2412 distance and dihedral restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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