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- PDB-2ase: NMR structure of the F28L mutant of Cdc42Hs -

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Basic information

Entry
Database: PDB / ID: 2ase
TitleNMR structure of the F28L mutant of Cdc42Hs
ComponentsCell division control protein 42 homolog
KeywordsSIGNALING PROTEIN / GTP binding protein / G-protein / cell signalling
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole ...GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / 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 / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / modulation by host of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / 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 / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / 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 mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / 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 / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule / small monomeric GTPase / actin filament organization / positive regulation of DNA replication / integrin-mediated signaling pathway / filopodium / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / RHO GTPases Activate Formins / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / G beta:gamma signalling through CDC42 / endocytosis / mitotic spindle / ubiquitin protein ligase activity / positive regulation of neuron apoptotic process / apical part of cell / intracellular protein localization
Similarity search - Function
Cdc42 / 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 ...Cdc42 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, simulated annealing
AuthorsAdams, P.D. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2006
Title: Solution Structure of an Oncogenic Mutant of Cdc42Hs
Authors: Adams, P.D. / Oswald, R.E.
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)19,7411
Polymers19,7411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 19740.689 Da / Num. of mol.: 1 / Mutation: F28L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: PGEX-CDC42HSF28L / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60953

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
13115N-HSQC
14215N-HSQC
1532D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N Cdc42Hs, 25 mM phosphate buffer, 5 mM MgCl2, pH 5.5, 90% H2O, 10% D2O90% H2O/10% D2O
2U-15N Cdc42Hs, 25 mM phosphate buffer, 5 mM MgCl2, pH 5.5, 100% D2O100% D2O
3Cdc42Hs, 25 mM phosphate buffer, 5 mM MgCl2, pH 5.5, 100% D2O100% D2O
Sample conditionsIonic strength: 30 mM / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR softwareName: XPLOR-NIH / Version: 2.9.0 / Classification: refinement
RefinementMethod: Distance geometry, simulated annealing / Software ordinal: 1
Details: The structure was determined using 978 distance restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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