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- PDB-1aje: CDC42 FROM HUMAN, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1aje
TitleCDC42 FROM HUMAN, NMR, 20 STRUCTURES
ComponentsCDC42HS
KeywordsG-PROTEIN / CELLULAR SIGNALING / CYTOSKELETAL REARRANGEMENT
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process ...GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / Cdc42 protein signal transduction / 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 / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / GTP-dependent protein binding / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / positive regulation of intracellular protein transport / neuropilin signaling pathway / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / thioesterase binding / embryonic heart tube development / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / DCC mediated attractive signaling / sprouting angiogenesis / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / phagocytosis, engulfment / establishment or maintenance of cell polarity / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / 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 / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / RAC1 GTPase cycle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / positive regulation of DNA replication / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / G protein activity / Regulation of actin dynamics for phagocytic cup formation / mitotic spindle / cellular response to type II interferon / G beta:gamma signalling through CDC42 / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity / cell-cell junction
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
AuthorsFeltham, J.L. / Dotsch, V. / Raza, S. / Manor, D. / Cerione, R.A. / Sutcliffe, M.J. / Wagner, G. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 1997
Title: Definition of the switch surface in the solution structure of Cdc42Hs.
Authors: Feltham, J.L. / Dotsch, V. / Raza, S. / Manor, D. / Cerione, R.A. / Sutcliffe, M.J. / Wagner, G. / Oswald, R.E.
History
DepositionMay 2, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: CDC42HS


Theoretical massNumber of molelcules
Total (without water)21,5131
Polymers21,5131
Non-polymers00
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 / 50LOWEST OVERALL ENERGY AND LOWEST CONSTRAINT VIOLATIONS
Representative

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Components

#1: Protein CDC42HS


Mass: 21512.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SEVEN NON-NATIVE AMINO ACIDS REMAIN AT THE N-TERMINUS AFTER CLEAVAGE OF THE FUSION PROTEIN
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: MEMBRANES AND GOLGI / Organ: PLACENTA / Plasmid: PGEX-CDC42HS / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TG1, BL21 AND DL39 / References: UniProt: P60953

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HSQC
141HNCO
151HNCA
161HN(CO)CA
171CBCA(CO)NH
181HCACO
191TOCSY-HSQC
1101(H)CCH-TOCSY
1111NOESY-HSQC
1121HMQC-NOESY-HMQC

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY (500 MHZ)VarianUNITY (500 MHZ)4001
Varian UNITY INOVA (600 MHZVarianUNITY INOVA (600 MHZ5002
Varian UNITY PLUS (400VarianUNITY PLUS (4006003
Varian 750 MHZ)Varian750 MHZ)7004

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
X-PLOR3.843structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST OVERALL ENERGY AND LOWEST CONSTRAINT VIOLATIONS
Conformers calculated total number: 50 / Conformers submitted total number: 20

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