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- PDB-1cf4: CDC42/ACK GTPASE-BINDING DOMAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1cf4
TitleCDC42/ACK GTPASE-BINDING DOMAIN COMPLEX
Components
  • PROTEIN (ACTIVATED P21CDC42HS KINASE)
  • PROTEIN (CDC42 HOMOLOG)
KeywordsTRANSFERASE / CDC42-ACK GTPASE COMPLEX / G PROTEIN
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / Grb2-EGFR complex / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cytoophidium / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole ...regulation of clathrin-dependent endocytosis / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / Grb2-EGFR complex / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cytoophidium / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / GTPase inhibitor activity / 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 / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / 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 / phosphorylation / DCC mediated attractive signaling / regulation of postsynapse organization / clathrin-coated vesicle / Signaling by LTK / CD28 dependent Vav1 pathway / epidermal growth factor receptor binding / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / positive regulation of peptidyl-tyrosine phosphorylation / regulation of mitotic nuclear division / WW domain binding / nuclear migration / phagocytosis, engulfment / RHOV GTPase cycle / 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 / 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 / clathrin-coated pit / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / protein serine/threonine/tyrosine kinase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / actin filament organization / small monomeric GTPase / integrin-mediated signaling pathway / filopodium / adherens junction / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42
Similarity search - Function
Activated P21cdc42hs Kinase; Chain B / Cdc42-like binding domain / Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : ...Activated P21cdc42hs Kinase; Chain B / Cdc42-like binding domain / Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like / Cdc42 / Variant SH3 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Few Secondary Structures / Irregular / Small GTP-binding protein domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / P-loop containing nucleotide triphosphate hydrolases / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsMott, H.R. / Owen, D. / Nietlispach, D. / Lowe, P.N. / Lim, L. / Laue, E.D.
CitationJournal: Nature / Year: 1999
Title: Structure of the small G protein Cdc42 bound to the GTPase-binding domain of ACK.
Authors: Mott, H.R. / Owen, D. / Nietlispach, D. / Lowe, P.N. / Manser, E. / Lim, L. / Laue, E.D.
History
DepositionMar 23, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 18, 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 ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_refine.details / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.version / _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.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.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_ref_seq_dif.details / _struct_sheet.number_strands / _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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CDC42 HOMOLOG)
B: PROTEIN (ACTIVATED P21CDC42HS KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8294
Polymers25,2832
Non-polymers5472
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #19medoid

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Components

#1: Protein PROTEIN (CDC42 HOMOLOG)


Mass: 20438.555 Da / Num. of mol.: 1 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#2: Protein/peptide PROTEIN (ACTIVATED P21CDC42HS KINASE)


Mass: 4844.192 Da / Num. of mol.: 1 / Fragment: GTPASE-BINDING DOMAIN / Source method: isolated from a natural source / Details: COMPLEXED WITH 5'-GUANOSYL-IMIDO-TRIPHOSPHATE / Source: (natural) Homo sapiens (human) / References: UniProt: Q07912
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateType
111isotropic3D HNCA
121isotropic3D HNCO
134isotropic3D (H)CCH-TOCSY
145isotropic15N-edited NOESY
152isotropic15N-edited NOESY
162isotropic15N-edited TOCSY
173isotropic3D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1[50%2H; 100%15N,13C]-labelled Cdc42, unlabelled f-ACK, 90% H2O/10%5 mM Na2HPO4, pH 5.5 25 mM NaCl, 5 mM MgCl2, 5 mM DTTsample_190% H2O/10% D2O
solution2[U-15N] f-ACK, Cdc42, 90% H2O/10%5 mM Na2HPO4, pH 5.5 25 mM NaCl, 5 mM MgCl2, 5 mM DTTsample_290% H2O/10% D2O
solution3[U-13C; U-15N] f-ACK, Cdc42, 90% H2O/10% D2O5 mM Na2HPO4, pH 5.5 25 mM NaCl, 5 mM MgCl2, 5 mM DTTsample_390% H2O/10% D2O
solution4[U-13C; U-15N] Cdc42, 90% H2O/10% D2O5 mM Na2HPO4, pH 5.5 25 mM NaCl, 5 mM MgCl2, 5 mM DTTsample_490% H2O/10% D2O
solution5[U-100% 15N] Cdc42, 90% H2O/10% D2O5 mM Na2HPO4, pH 5.5 25 mM NaCl, 5 mM MgCl2, 5 mM DTTsample_590% H2O/10% D2O
Sample
ComponentIsotopic labelingSolution-ID
Cdc42[50%2H; 100%15N,13C]1
f-ACKnatural abundance1
f-ACK[U-15N]2
Cdc42natural abundance2
f-ACK[U-13C; U-15N]3
Cdc42natural abundance3
Cdc42[U-13C; U-15N]4
Cdc42[U-100% 15N]5
Sample conditionspH: 5.5 / Temperature: 298.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
ANSIGKRAULISstructure calculation
XPLOR3.851BRUNGERstructure calculation
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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