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- PDB-1cee: SOLUTION STRUCTURE OF CDC42 IN COMPLEX WITH THE GTPASE BINDING DO... -

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Basic information

Entry
Database: PDB / ID: 1cee
TitleSOLUTION STRUCTURE OF CDC42 IN COMPLEX WITH THE GTPASE BINDING DOMAIN OF WASP
Components
  • GTP-BINDING RHO-LIKE PROTEIN
  • WISKOTT-ALDRICH SYNDROME PROTEIN WASP
KeywordsStructural protein Regulation / CDC42 ACTIN REGULATOR GTPASE AND THE GTPASE BINDING DOMAIN OF ITS EFFECTOR WASP
Function / homology
Function and homology information


regulation of T cell antigen processing and presentation / Cdc42 protein signal transduction / GBD domain binding / positive regulation of pinocytosis / COG complex / regulation of actin polymerization or depolymerization / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / GTPase regulator activity / storage vacuole ...regulation of T cell antigen processing and presentation / Cdc42 protein signal transduction / GBD domain binding / positive regulation of pinocytosis / COG complex / regulation of actin polymerization or depolymerization / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / GTPase regulator activity / storage vacuole / dendritic cell migration / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / Inactivation of CDC42 and RAC1 / positive regulation of pseudopodium assembly / host-mediated perturbation of viral process / regulation of filopodium assembly / cardiac conduction system development / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / actin filament-based movement / filopodium assembly / cell junction assembly / dendritic spine morphogenesis / establishment of epithelial cell apical/basal polarity / adherens junction organization / GTP-dependent protein binding / negative regulation of stress fiber assembly / thioesterase binding / negative regulation of cell motility / regulation of lamellipodium assembly / actin polymerization or depolymerization / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / vesicle membrane / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / endosomal transport / RHOV GTPase cycle / regulation of mitotic nuclear division / Myogenesis / nuclear migration / small GTPase-mediated signal transduction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / heart contraction / RHOQ GTPase cycle / establishment of cell polarity / Golgi organization / RHOU GTPase cycle / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / CDC42 GTPase cycle / Generation of second messenger molecules / macrophage differentiation / RHOG GTPase cycle / epidermis development / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of double-strand break repair via homologous recombination / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phospholipase binding / phagocytic vesicle / positive regulation of stress fiber assembly / RAC1 GTPase cycle / actin filament polymerization / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / T cell activation / small monomeric GTPase / integrin-mediated signaling pathway / actin filament organization / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / actin filament / EGFR downregulation / defense response / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / MAPK6/MAPK4 signaling / VEGFA-VEGFR2 Pathway / cellular response to type II interferon
Similarity search - Function
SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Cdc42 / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH2 domain / WH1 domain ...SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Cdc42 / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH2 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. / 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 / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Actin nucleation-promoting factor WAS / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsAbdul-Manan, N. / Aghazadeh, B. / Liu, G.A. / Majumdar, A. / Ouerfelli, O. / Rosen, M.K.
CitationJournal: Nature / Year: 1999
Title: Structure of Cdc42 in complex with the GTPase-binding domain of the 'Wiskott-Aldrich syndrome' protein.
Authors: Abdul-Manan, N. / Aghazadeh, B. / Liu, G.A. / Majumdar, A. / Ouerfelli, O. / Siminovitch, K.A. / Rosen, M.K.
History
DepositionMar 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: GTP-BINDING RHO-LIKE PROTEIN
B: WISKOTT-ALDRICH SYNDROME PROTEIN WASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8094
Polymers26,2642
Non-polymers5462
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 / 80LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein GTP-BINDING RHO-LIKE PROTEIN / CELL DIVISION CYCLE 42 / PCDC42


Mass: 19871.820 Da / Num. of mol.: 1 / Fragment: CDC42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P60953
#2: Protein WISKOTT-ALDRICH SYNDROME PROTEIN WASP


Mass: 6392.066 Da / Num. of mol.: 1 / Fragment: GTPASE BINDING DOMAIN OF WASP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42768
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY TOCSY 2D AND 3D THROUGH BOND TRANSFER EXPERIMENTS
12113C/15N PURGED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING A COMBINATION OF TRIPLE- AND QUADRUPLE- RESONANCE NMR EXPERIMENTS ON 13C/ 15N AND PARTIALLY OR FULLY DEUTERATED SAMPLES WITH SELECTIVE METHYL LABELING AT ...Text: THE STRUCTURE WAS DETERMINED USING A COMBINATION OF TRIPLE- AND QUADRUPLE- RESONANCE NMR EXPERIMENTS ON 13C/ 15N AND PARTIALLY OR FULLY DEUTERATED SAMPLES WITH SELECTIVE METHYL LABELING AT VALINE,LUECINE AND ISOLEUCINES.

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Sample preparation

Sample conditionsIonic strength: 50mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.3A.BRUNGER, M.NILGESrefinement
NMRPipestructure solution
NMRViewstructure solution
ARIAstructure solution
X-PLORstructure solution
CNSstructure solution
X-PLOR3.1BRUNGERrefinement
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: X-PLOR 3.851 WAS USED IN COMBINATION WITH ARIA (REF. M. NILGES)
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 80 / Conformers submitted total number: 20

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