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- PDB-2w2v: Rac2 (G12V) in complex with GTPgS -

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Basic information

Entry
Database: PDB / ID: 2w2v
TitleRac2 (G12V) in complex with GTPgS
ComponentsRAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
KeywordsSIGNALING PROTEIN / ADP-RIBOSYLATION / CYTOPLASM / DISEASE MUTATION / GTP-BINDING / LIPOPROTEIN / METHYLATION / NUCLEOTIDE-BINDING / POLYMORPHISM / PRENYLATION / PHOSPHOLIPASE C / PHOSPHOINOSITIDES / RHO
Function / homology
Function and homology information


regulation of mast cell chemotaxis / lymphocyte aggregation / regulation of cell-substrate adhesion / erythrocyte enucleation / positive regulation of mast cell proliferation / regulation of respiratory burst / mast cell proliferation / regulation of mast cell degranulation / regulation of neutrophil migration / regulation of hydrogen peroxide metabolic process ...regulation of mast cell chemotaxis / lymphocyte aggregation / regulation of cell-substrate adhesion / erythrocyte enucleation / positive regulation of mast cell proliferation / regulation of respiratory burst / mast cell proliferation / regulation of mast cell degranulation / regulation of neutrophil migration / regulation of hydrogen peroxide metabolic process / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / cell projection assembly / ROS and RNS production in phagocytes / PCP/CE pathway / protein kinase regulator activity / positive regulation of neutrophil chemotaxis / superoxide anion generation / positive regulation of protein targeting to mitochondrion / small GTPase-mediated signal transduction / establishment or maintenance of cell polarity / regulation of T cell proliferation / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / bone resorption / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / small monomeric GTPase / actin filament organization / cell projection / regulation of actin cytoskeleton organization / phagocytic vesicle membrane / chemotaxis / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear envelope / PIP3 activates AKT signaling / lamellipodium / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / mitochondrial outer membrane / cytoskeleton / G protein-coupled receptor signaling pathway / focal adhesion / GTPase activity / endoplasmic reticulum membrane / protein kinase binding / GTP binding / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related C3 botulinum toxin substrate 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,0588
Polymers80,9654
Non-polymers2,0934
Water9,494527
1
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,2411
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,2411
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,2411
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,2411
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.202, 94.529, 107.237
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 / RAC2 / P21-RAC2 / SMALL G PROTEIN / GX


Mass: 20241.234 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-177 / 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLY 12 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN C, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN D, GLY 12 TO VAL
Sequence detailsTHERE IS TAG LINKER SEQUENCE, GGGSGGS (NOT SEEN) AND A 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7
Details: RAC2(2-177)GTPGS WAS CRYSTALLIZED USING A PROTEIN CONCENTRATION OF 25 MG/ML WITH PRECIPITANT (18% PEG3350, 300 MM SODIUM/POTASSIUM TARTRATE) AND AT A CONSTANT TEMPERATURE OF 20C

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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 % / Biso Wilson estimate: 20.98 Å2 / 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 RAC2 STRUCTURE

Resolution: 2→53.62 Å / SU ML: 0.45 / σ(F): 1.12 / Phase error: 40.6 / Stereochemistry target values: ML
Details: DATA INITIALLY THOUGHT TO BE P212121, LATER FOUND TO BE P21 WITH B AS 90, ALSO TWINNED.
RfactorNum. reflection% reflection
Rfree0.345 4720 5.1 %
Rwork0.28 --
obs0.283 92859 82.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.57 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.9782 Å20 Å20.7393 Å2
2--23.0459 Å20 Å2
3----14.0677 Å2
Refinement stepCycle: LAST / Resolution: 2→53.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5156 0 128 527 5811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025442
X-RAY DIFFRACTIONf_angle_d0.6417478
X-RAY DIFFRACTIONf_dihedral_angle_d18.5441907
X-RAY DIFFRACTIONf_chiral_restr0.042894
X-RAY DIFFRACTIONf_plane_restr0.003921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.41491380.39682645X-RAY DIFFRACTION74
2.0227-2.04650.48331410.41612751X-RAY DIFFRACTION79
2.0465-2.07150.47141620.39962794X-RAY DIFFRACTION79
2.0715-2.09770.44841620.38192819X-RAY DIFFRACTION78
2.0977-2.12530.44011570.37182757X-RAY DIFFRACTION79
2.1253-2.15440.40931350.36192771X-RAY DIFFRACTION79
2.1544-2.18520.37061420.33842837X-RAY DIFFRACTION79
2.1852-2.21780.41151560.32822837X-RAY DIFFRACTION80
2.2178-2.25250.44751530.36022752X-RAY DIFFRACTION78
2.2525-2.28940.3751250.32442804X-RAY DIFFRACTION80
2.2894-2.32890.35221550.31772943X-RAY DIFFRACTION81
2.3289-2.37120.40491790.30372766X-RAY DIFFRACTION80
2.3712-2.41690.37341550.29412843X-RAY DIFFRACTION81
2.4169-2.46620.30811630.28372939X-RAY DIFFRACTION82
2.4662-2.51980.37071500.28842884X-RAY DIFFRACTION81
2.5198-2.57840.35631650.30862901X-RAY DIFFRACTION83
2.5784-2.64290.40881210.33073066X-RAY DIFFRACTION84
2.6429-2.71440.39111630.29862898X-RAY DIFFRACTION84
2.7144-2.79420.36311390.30593046X-RAY DIFFRACTION85
2.7942-2.88440.39061480.30193036X-RAY DIFFRACTION86
2.8844-2.98750.4081820.29433049X-RAY DIFFRACTION86
2.9875-3.10710.3641580.27623066X-RAY DIFFRACTION87
3.1071-3.24850.34881800.2533181X-RAY DIFFRACTION88
3.2485-3.41970.29581800.24022988X-RAY DIFFRACTION87
3.4197-3.63390.28081790.24183103X-RAY DIFFRACTION87
3.6339-3.91440.31471460.23143144X-RAY DIFFRACTION89
3.9144-4.30820.25241660.22863147X-RAY DIFFRACTION88
4.3082-4.93130.27072050.19913092X-RAY DIFFRACTION88
4.9313-6.21140.27861630.23133162X-RAY DIFFRACTION89
6.2114-53.63750.28981520.22593118X-RAY DIFFRACTION87

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