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- PDB-2kb0: Cdc42(T35A) -

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Basic information

Entry
Database: PDB / ID: 2kb0
TitleCdc42(T35A)
ComponentsCell division control protein 42 homolog
KeywordsSIGNALING PROTEIN / globular / folded / Switch 1 / mutation / Ras / Alternative splicing / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation
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 / DGSA-distance geometry simulated annealing
AuthorsAdams, P.D. / Oswald, R.E. / McFeeters, R.
CitationJournal: To be Published
Title: Cdc42(T35A)
Authors: Adams, P. / Oswald, R. / McFeeters, R.
History
DepositionNov 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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)19,7451
Polymers19,7451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 18structures 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: 19744.678 Da / Num. of mol.: 1 / Mutation: T35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] Cdc42(T35A), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.4 mM / Component: Cdc42(T35A) / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian AMX / Manufacturer: Varian / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: nih-xplor used to calculate structures
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 18 / Conformers submitted total number: 12

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