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- PDB-2ee5: Solution structure of the N-teruminus extended RhoGAP domain from... -

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Basic information

Entry
Database: PDB / ID: 2ee5
TitleSolution structure of the N-teruminus extended RhoGAP domain from human Rho GTPase activating protein 5 variant
ComponentsRho GTPase activating protein 5 variant
KeywordsHYDROLASE / all alpha protein / GTPase-activating protein for Rho family members / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


epithelial cell migration / mammary gland development / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of mesenchymal cell proliferation / regulation of cell size ...epithelial cell migration / mammary gland development / RHOF GTPase cycle / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of mesenchymal cell proliferation / regulation of cell size / RHOB GTPase cycle / positive regulation of epithelial cell migration / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / SH2 domain binding / GTPase activator activity / cell adhesion / GTPase activity / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein ...Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 5 / Rho GTPase-activating protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the N-teruminus extended RhoGAP domain from human Rho GTPase activating protein 5 variant
Authors: Tomizawa, T. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GTPase activating protein 5 variant


Theoretical massNumber of molelcules
Total (without water)25,1871
Polymers25,1871
Non-polymers00
Water0
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 least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Rho GTPase activating protein 5 variant


Mass: 25186.547 Da / Num. of mol.: 1 / Fragment: RhoGAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P060123-15
References: UniProt: Q59ER0, UniProt: Q13017*PLUS, small monomeric GTPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.31mM RhoGAP domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCE IIBrukerAVANCE II9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
TopSpin1.3Brukercollection
NMRPipe20060524Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9823Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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