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- PDB-1x0h: Solution structure of the carboxyl-terminal RGC domain in human IQGAP1 -

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Entry
Database: PDB / ID: 1x0h
TitleSolution structure of the carboxyl-terminal RGC domain in human IQGAP1
ComponentsRas GTPase-activating-like protein IQGAP1
KeywordsSIGNALING PROTEIN / cell adhesion / beta-sandwich / protein-protein interaction / structural genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


negative regulation of dephosphorylation / mitotic actomyosin contractile ring assembly actin filament organization / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions / neuron projection extension ...negative regulation of dephosphorylation / mitotic actomyosin contractile ring assembly actin filament organization / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions / neuron projection extension / RHOV GTPase cycle / cortical actin cytoskeleton / RHOC GTPase cycle / RHOQ GTPase cycle / cellular response to platelet-derived growth factor stimulus / phosphatidylinositol-3,4,5-trisphosphate binding / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / CDC42 GTPase cycle / lateral plasma membrane / fibroblast growth factor receptor signaling pathway / RHOA GTPase cycle / positive regulation of protein kinase activity / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / ruffle / regulation of mitotic cell cycle / regulation of cytokine production / cellular response to epidermal growth factor stimulus / RAC1 GTPase cycle / cellular response to calcium ion / GTPase activator activity / protein serine/threonine kinase activator activity / secretory granule membrane / actin filament / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / small GTPase binding / cytoplasmic side of plasma membrane / cytoplasmic ribonucleoprotein granule / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / actin filament binding / cell migration / cell cortex / midbody / growth cone / basolateral plasma membrane / protein phosphatase binding / microtubule / positive regulation of MAPK cascade / molecular adaptor activity / calmodulin binding / neuron projection / cadherin binding / ribonucleoprotein complex / apical plasma membrane / protein domain specific binding / axon / focal adhesion / calcium ion binding / Neutrophil degranulation / protein kinase binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain ...RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras GTPase-activating-like protein IQGAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the carboxyl-terminal RGC domain in human IQGAP1
Authors: Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)12,5651
Polymers12,5651
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ras GTPase-activating-like protein IQGAP1 / p195


Mass: 12565.481 Da / Num. of mol.: 1 / Fragment: RGC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA ha00940 / Plasmid: P040816-19 / References: UniProt: P46940

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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 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM protein, 20mM sodium phosphate buffer, pH6.0, 200mM NaCl, 1mM d-DTT, 50mM L-arginine, 50mM L-glutamic acid
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 220 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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