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- PDB-2k85: p190-A RhoGAP FF1 domain -

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Basic information

Entry
Database: PDB / ID: 2k85
Titlep190-A RhoGAP FF1 domain
ComponentsGlucocorticoid receptor DNA-binding factor 1
KeywordsPROTEIN BINDING / FF domain / p190-A RhoGAP / protein phosphorylation / Alternative splicing / Anti-oncogene / Cell cycle / Cytoplasm / DNA-binding / GTPase activation / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


central nervous system neuron axonogenesis / neuron projection guidance / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / mammary gland development / positive regulation of cilium assembly / camera-type eye development / negative regulation of vascular permeability / RHOD GTPase cycle / axonal fasciculation ...central nervous system neuron axonogenesis / neuron projection guidance / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / mammary gland development / positive regulation of cilium assembly / camera-type eye development / negative regulation of vascular permeability / RHOD GTPase cycle / axonal fasciculation / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / wound healing, spreading of cells / RND2 GTPase cycle / RND3 GTPase cycle / negative regulation of Rho protein signal transduction / regulation of cell size / RHOB GTPase cycle / regulation of axonogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / Rho protein signal transduction / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / forebrain development / RAC1 GTPase cycle / GTPase activator activity / ciliary basal body / axon guidance / neural tube closure / regulation of actin cytoskeleton organization / phospholipid binding / positive regulation of neuron projection development / cell migration / actin cytoskeleton / regulation of cell shape / GTPase activity / GTP binding / DNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / Rho GTPase-activating protein, pG1 and pG2 domain / : / p190-A and -B Rho GAPs FF domain / p190RhoGAP, pG1 and pG2 domains / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain ...Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / Rho GTPase-activating protein, pG1 and pG2 domain / : / p190-A and -B Rho GAPs FF domain / p190RhoGAP, pG1 and pG2 domains / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / 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 / Small GTPase / Ras family / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho GTPase-activating protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBonet, R. / Ruiz, L. / Martin-Malpartida, P. / Macias, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: NMR structural studies on human p190-A RhoGAPFF1 revealed that domain phosphorylation by the PDGF-receptor alpha requires its previous unfolding.
Authors: Bonet, R. / Ruiz, L. / Aragon, E. / Martin-Malpartida, P. / Macias, M.J.
History
DepositionSep 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucocorticoid receptor DNA-binding factor 1


Theoretical massNumber of molelcules
Total (without water)8,1731
Polymers8,1731
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 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Glucocorticoid receptor DNA-binding factor 1 / Glucocorticoid receptor repression factor 1 / GRF-1 / Rho GAP p190A / p190-A


Mass: 8173.325 Da / Num. of mol.: 1 / Fragment: UNP residues 267-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: contains a His-tag, a thioredoxin fusion protein and a TEV cleavage-site
Gene: GRLF1, GRF1, KIAA1722 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NRY4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: p190-A RhoGAP FF1 domain from homo sapiens
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D 1H-15N NOESY
1623D HNHA
1733D (H)CCH-TOCSY
1833D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM p190-A RhoGAP FF1 domain, 50 mM sodium phosphate, 150 mM sodium chloride, 0.5 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] p190-A RhoGAP FF1 domain, 50 mM sodium phosphate, 150 mM sodium chloride, 0.5 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C; U-100% 15N] p190-A RhoGAP FF1 domain, 50 mM sodium phosphate, 150 mM sodium chloride, 0.5 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMp190-A RhoGAP FF1 domain1
50 mMsodium phosphate1
150 mMsodium chloride1
0.5 mMsodium azide1
0.5 mMp190-A RhoGAP FF1 domain[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate2
150 mMsodium chloride2
0.5 mMsodium azide2
0.5 mMp190-A RhoGAP FF1 domain[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate3
150 mMsodium chloride3
0.5 mMsodium azide3
Sample conditionsIonic strength: 0.2 / pH: 7.2 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIABrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIABrunger, Adams, Clore, Gros, Nilges and Readrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 15

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