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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 PROTEIN
  • P21-ACTIVATED KINASE
KeywordsSTRUCTURAL PROTEIN / protein-protein complex
Function / homology
Function and homology information


CD28 dependent Vav1 pathway / Ephrin signaling / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / RHO GTPases activate PAKs / GBD domain binding / Generation of second messenger molecules / Golgi transport complex / positive regulation of pinocytosis / VEGFR2 mediated vascular permeability ...CD28 dependent Vav1 pathway / Ephrin signaling / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / RHO GTPases activate PAKs / GBD domain binding / Generation of second messenger molecules / Golgi transport complex / positive regulation of pinocytosis / VEGFR2 mediated vascular permeability / RAC1 GTPase cycle / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / 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 / cardiac conduction system development / host-mediated perturbation of viral process / dendritic spine development / CD209 (DC-SIGN) signaling / regulation of filopodium assembly / regulation of actin filament polymerization / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / Myogenesis / positive regulation of cytokinesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / dendrite development / MAP kinase kinase activity / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / actin filament organization / EGFR downregulation / small monomeric GTPase / integrin-mediated signaling pathway / MAPK6/MAPK4 signaling / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis
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 ...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 domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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
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: GTP-BINDING PROTEIN
B: P21-ACTIVATED KINASE


Theoretical massNumber of molelcules
Total (without water)24,8922
Polymers24,8922
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 / 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 / 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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