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- PDB-2ije: Crystal Structure of the Cdc25 domain of RasGRF1 -

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Basic information

Entry
Database: PDB / ID: 2ije
TitleCrystal Structure of the Cdc25 domain of RasGRF1
ComponentsGuanine nucleotide-releasing protein
KeywordsSIGNALING PROTEIN / RasGRF1 / Cdc25 Domain / Ras Guanine Nucleotide Releasing Factor / Ras-specific Nucleotide Exchange Factor
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / regulation of Ras protein signal transduction / RAF/MAP kinase cascade / : / regulation of Rac protein signal transduction / apicolateral plasma membrane / apical dendrite / regulation of Rho protein signal transduction / positive regulation of Ras protein signal transduction ...guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / regulation of Ras protein signal transduction / RAF/MAP kinase cascade / : / regulation of Rac protein signal transduction / apicolateral plasma membrane / apical dendrite / regulation of Rho protein signal transduction / positive regulation of Ras protein signal transduction / activation of GTPase activity / regulation of NMDA receptor activity / small GTPase-mediated signal transduction / regulation of neuronal synaptic plasticity / glutamate receptor binding / response to endoplasmic reticulum stress / positive regulation of GTPase activity / regulation of synaptic plasticity / receptor tyrosine kinase binding / neuron projection development / positive regulation of fibroblast proliferation / growth cone / basolateral plasma membrane / cell population proliferation / neuronal cell body / protein kinase binding / cytoplasm / cytosol
Similarity search - Function
Ras-specific guanine nucleotide-releasing factor 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal ...Ras-specific guanine nucleotide-releasing factor 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / IQ motif profile. / IQ motif, EF-hand binding site / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ras-specific guanine nucleotide-releasing factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFreedman, T.S. / Kuriyan, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: A Ras-induced conformational switch in the Ras activator Son of sevenless.
Authors: Freedman, T.S. / Sondermann, H. / Friedland, G.D. / Kortemme, T. / Bar-Sagi, D. / Marqusee, S. / Kuriyan, J.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: Guanine nucleotide-releasing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9352
Polymers27,8431
Non-polymers921
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.430, 77.801, 110.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Guanine nucleotide-releasing protein / GNRP / Ras-specific nucleotide exchange factor CDC25 / CDC25Mm


Mass: 27843.102 Da / Num. of mol.: 1 / Fragment: Cdc25 Domain (residues 1028-1262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: 19417 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3* / References: UniProt: P27671
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 1:1 Mixture of Well Solution: 0.1 M Sodium Acetate, pH 5.2, 3% PEG 4000, 0.5% beta-octylglucoside. Protein Stock: 10 mg/ml RasGRF1, 10% Glycerol, 5 mM TCEP, 25 mM Tris, pH 8.0, 200 mM Sodium ...Details: 1:1 Mixture of Well Solution: 0.1 M Sodium Acetate, pH 5.2, 3% PEG 4000, 0.5% beta-octylglucoside. Protein Stock: 10 mg/ml RasGRF1, 10% Glycerol, 5 mM TCEP, 25 mM Tris, pH 8.0, 200 mM Sodium Chloride. Cryoprotection: Dip in Well solution with 30% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.974
DetectorDetector: CCD / Date: May 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17115 / Num. obs: 17115 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1695 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NVV

1nvv


Resolution: 2.2→50 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1533 -RANDOM
Rwork0.2 ---
all0.205 16832 --
obs0.205 15478 92 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.237 Å20 Å20 Å2
2--5.959 Å20 Å2
3----3.722 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 6 163 2103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.19484
X-RAY DIFFRACTIONc_bond_d0.007613
LS refinement shellResolution: 2.2→2.22 Å
RfactorNum. reflection
Rfree0.3412 52
Rwork0.2721 -
obs-439

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