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- PDB-1e0a: Cdc42 complexed with the GTPase binding domain of p21 activated kinase -

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Basic information

Entry
Database: PDB / ID: 1e0a
TitleCdc42 complexed with the GTPase binding domain of p21 activated kinase
Components
  • Cell division control protein 42 homolog
  • Serine/threonine-protein kinase PAK 1
KeywordsSIGNALLING PROTEIN/KINASE / SIGNALLING PROTEIN / G PROTEIN SIGNALLING SER/THR KINASE / SIGNALLING PROTEIN-KINASE COMPLEX
Function / homology
Function and homology information


CD28 dependent Vav1 pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / CD209 (DC-SIGN) signaling / Generation of second messenger molecules / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / RAC2 GTPase cycle ...CD28 dependent Vav1 pathway / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / CD209 (DC-SIGN) signaling / Generation of second messenger molecules / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / RAC2 GTPase cycle / MAPK6/MAPK4 signaling / RHOH GTPase cycle / Smooth Muscle Contraction / RHOQ GTPase cycle / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / RAC1 GTPase cycle / negative regulation of cell proliferation involved in contact inhibition / observational learning / GBD domain binding / submandibular salivary gland formation / Golgi transport complex / amygdala development / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / Regulation of actin dynamics for phagocytic cup formation / gamma-aminobutyric acid secretion, neurotransmission / Signal transduction by L1 / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / glutamate secretion, neurotransmission / protein localization to cytoplasmic stress granule / FCERI mediated MAPK activation / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / modulation by host of viral process / dendritic spine development / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / positive regulation of microtubule nucleation / neuropilin signaling pathway / EPHB-mediated forward signaling / positive regulation of intracellular protein transport / hepatocyte growth factor receptor signaling pathway / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / regulation of lamellipodium assembly / G beta:gamma signalling through CDC42 / gamma-tubulin binding / positive regulation of vascular associated smooth muscle cell migration / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / regulation of long-term synaptic potentiation / DCC mediated attractive signaling / positive regulation of fibroblast migration / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / nuclear migration / regulation of axonogenesis / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / branching morphogenesis of an epithelial tube / small GTPase-mediated signal transduction / positive regulation of intracellular estrogen receptor signaling pathway / neuromuscular junction development / Myogenesis / heart contraction / receptor clustering / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / transmission of nerve impulse / positive regulation of cytokinesis / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / dendrite development
Similarity search - Function
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 ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Serine/threonine-protein kinase PAK 1 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / DISTANCE GEOMETRY OF A SUBSTRUCTURE, CARTESIAN DYNAMICS
AuthorsMorreale, A. / Venkatesan, M. / Mott, H.R. / Owen, D. / Nietlispach, D. / Lowe, P.N. / Laue, E.D.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Solution Structure of Cdc42 Bound to the Gtpase Binding Domian of Pak
Authors: Morreale, A. / Venkatesan, M. / Mott, H.R. / Owen, D. / Nietlispach, D. / Lowe, P.N. / Laue, E.D.
History
DepositionMar 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Feb 5, 2014Group: Source and taxonomy
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_nmr_software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO ... SHEET DETERMINATION METHOD: THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3 AND 4 OF SHEET A1 AND A2 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 42 homolog
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0824
Polymers25,5352
Non-polymers5472
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100NO VIOLATIONS
RepresentativeModel #7

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Components

#1: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 20438.555 Da / Num. of mol.: 1 / Fragment: 1-184 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH 5'-GUANOSYL-IMIDO-TRIPHOSPHATE / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: CDC42 / Plasmid: PET16B / Cellular location (production host): CYTOPLASM / Gene (production host): CDC42 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60953, small monomeric GTPase
#2: Protein/peptide Serine/threonine-protein kinase PAK 1 / Alpha-PAK / Protein kinase MUK2 / p21-activated kinase 1 / PAK-1 / p68-PAK


Mass: 5096.617 Da / Num. of mol.: 1 / Fragment: 75-118 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASMIC / Gene: Pak1 / Plasmid: PGEX2T / Cellular location (production host): CYTOPLASM / Gene (production host): PAK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P35465, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A: ENGINEERED MUTATION GLN61LEU
Sequence detailsQ61L MUTANT. 7 C-TERMINAL RESIDUES REMOVED RESIDUES 73 AND 74 ARE FROM THE EXPRESSION SYSTEM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131TRIPLE RESONANCE EXPERIMENTS
141HNHA
NMR detailsText: SAMPLES WERE 13C,15N LABELLED CDC42 + UNLABELLED PAK OR 13C,15N LABELLED PAK + UNLABELLED CDC42

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Sample preparation

DetailsContents: 90% WATER, 10% D2O
Sample conditionsIonic strength: 5 MM NA2HPO4, 25MM NACL / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGERrefinement
Azarastructure solution
ANSIGstructure solution
CNSstructure solution
RefinementMethod: DISTANCE GEOMETRY OF A SUBSTRUCTURE, CARTESIAN DYNAMICS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20

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