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- PDB-1wfy: Solution structure of the Ras-binding domain of mouse RGS14 -

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Basic information

Entry
Database: PDB / ID: 1wfy
TitleSolution structure of the Ras-binding domain of mouse RGS14
Componentsregulator of G-protein signaling 14; rap1/rap2 interacting protein
KeywordsSIGNALING PROTEIN / Regulators of G-protein signaling / Ras family / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


zygote asymmetric cell division / negative regulation of synaptic plasticity / G alpha (i) signalling events / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / spindle organization / positive regulation of neurogenesis / negative regulation of G protein-coupled receptor signaling pathway ...zygote asymmetric cell division / negative regulation of synaptic plasticity / G alpha (i) signalling events / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / spindle organization / positive regulation of neurogenesis / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / G-protein alpha-subunit binding / long-term memory / negative regulation of MAP kinase activity / GTPase activator activity / positive regulation of GTPase activity / learning / chromosome segregation / long-term synaptic potentiation / modulation of chemical synaptic transmission / visual learning / PML body / negative regulation of ERK1 and ERK2 cascade / spindle pole / spindle / signaling receptor complex adaptor activity / mitotic cell cycle / microtubule binding / response to oxidative stress / microtubule / dendritic spine / postsynaptic density / nuclear body / G protein-coupled receptor signaling pathway / cell division / centrosome / glutamatergic synapse / dendrite / protein kinase binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / Regulator of G protein signaling domain ...RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Regulator of G-protein signaling 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsNakanishi, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Ras-binding domain of mouse RGS14
Authors: Nakanishi, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2004Provider: 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: regulator of G-protein signaling 14; rap1/rap2 interacting protein


Theoretical massNumber of molelcules
Total (without water)11,1701
Polymers11,1701
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 least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein regulator of G-protein signaling 14; rap1/rap2 interacting protein


Mass: 11169.587 Da / Num. of mol.: 1 / Fragment: Raf-like Ras-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 0610041O18 / Plasmid: P030120-12 / References: UniProt: P97492

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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 15N-separated NOESY

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Sample preparation

DetailsContents: 0.18mM RBD U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.87Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.structure solution
CYANA1.0.7Guntert, P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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