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- PDB-2w2t: Rac2 (G12V) in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2w2t
TitleRac2 (G12V) in complex with GDP
ComponentsRAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
KeywordsSIGNALING PROTEIN / PHOSPHOLIPASE C / PHOSPHOINOSITIDES / RHO GTPASES / RAC SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of mast cell chemotaxis / regulation of cell-substrate adhesion / lymphocyte aggregation / erythrocyte enucleation / positive regulation of mast cell proliferation / regulation of respiratory burst / regulation of neutrophil migration / mast cell proliferation / regulation of mast cell degranulation / NADPH oxidase complex ...regulation of mast cell chemotaxis / regulation of cell-substrate adhesion / lymphocyte aggregation / erythrocyte enucleation / positive regulation of mast cell proliferation / regulation of respiratory burst / regulation of neutrophil migration / mast cell proliferation / regulation of mast cell degranulation / NADPH oxidase complex / regulation of hydrogen peroxide metabolic process / respiratory burst / protein kinase regulator activity / ROS and RNS production in phagocytes / cell projection assembly / PCP/CE pathway / positive regulation of neutrophil chemotaxis / positive regulation of protein targeting to mitochondrion / small GTPase-mediated signal transduction / regulation of T cell proliferation / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / positive regulation of lamellipodium assembly / regulation of cell migration / bone resorption / GPVI-mediated activation cascade / actin filament organization / phagocytic vesicle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / chemotaxis / PIP3 activates AKT signaling / lamellipodium / nuclear envelope / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / mitochondrial outer membrane / G protein-coupled receptor signaling pathway / focal adhesion / GTPase activity / GTP binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Small GTPase Rho / small GTPase Rho family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOpaleye, O. / Bunney, T.D. / Roe, S.M. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Insights Into Formation of an Active Signaling Complex between Rac and Phospholipase C Gamma 2.
Authors: Bunney, T.D. / Opaleye, O. / Roe, S.M. / Vatter, P. / Baxendale, R.W. / Walliser, C. / Everett, K.L. / Josephs, M.B. / Christow, C. / Rodrigues-Lima, F. / Gierschik, P. / Pearl, L.H. / Katan, M.
History
DepositionNov 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7783
Polymers20,3101
Non-polymers4682
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.205, 98.106, 108.064
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 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 / P21-RAC2 / SMALL G PROTEIN / GX / RAC2


Mass: 20310.297 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-179 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P15153
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 12 TO VAL
Sequence detailsTHERE IS A LEADING LINKER SEQUENCE GGGSGGS (NOT SEEN IN STRUCTURE) AND MUTATION G12V

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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: 2.55 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7
Details: RAC2(2-192)GDP WAS CRYSTALLIZED USING A PROTEIN CONCENTRATION OF 20 MG/ML WITH PRECIPITANT (20% PEG3350, 100 MM BIS-TRIS PROPANE PH 7.0) AND AT A CONSTANT TEMPERATURE OF 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→54 Å / Num. obs: 79004 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE STRUCTURE.

Resolution: 1.95→54.03 Å / SU ML: 0.31 / σ(F): 1.21 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1535 5 %
Rwork0.207 --
obs0.21 30557 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.89 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.854 Å20 Å2-0 Å2
2--27.7227 Å2-0 Å2
3----18.1119 Å2
Refinement stepCycle: LAST / Resolution: 1.95→54.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 29 137 1502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231407
X-RAY DIFFRACTIONf_angle_d2.0481936
X-RAY DIFFRACTIONf_dihedral_angle_d19.078490
X-RAY DIFFRACTIONf_chiral_restr0.134231
X-RAY DIFFRACTIONf_plane_restr0.012242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.0130.35421420.35982446X-RAY DIFFRACTION90
2.013-2.0850.31721390.30282533X-RAY DIFFRACTION93
2.085-2.16850.29561410.28132563X-RAY DIFFRACTION94
2.1685-2.26720.33571410.2622585X-RAY DIFFRACTION95
2.2672-2.38670.35021500.23552621X-RAY DIFFRACTION97
2.3867-2.53620.25631310.2162728X-RAY DIFFRACTION98
2.5362-2.73210.28811230.21162720X-RAY DIFFRACTION100
2.7321-3.0070.24571350.20472721X-RAY DIFFRACTION99
3.007-3.4420.22571630.19242708X-RAY DIFFRACTION99
3.442-4.33630.23761600.16782683X-RAY DIFFRACTION99
4.3363-54.05280.17421100.16462714X-RAY DIFFRACTION98

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