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- PDB-2w2x: Complex of Rac2 and PLCg2 spPH Domain -

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Basic information

Entry
Database: PDB / ID: 2w2x
TitleComplex of Rac2 and PLCg2 spPH Domain
Components
  • (1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA- ...) x 2
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
KeywordsSIGNALING PROTEIN/HYDROLASE / HYDROLASE / PHOSPHOLIPASE C / PHOSPHOINOSITIDES / RHO GTPASES / RAC / SH2 DOMAIN / SH3 DOMAIN / SIGNALING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


regulation of mast cell chemotaxis / regulation of cell-substrate adhesion / lymphocyte aggregation / follicular B cell differentiation / inositol trisphosphate biosynthetic process / erythrocyte enucleation / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / positive regulation of mast cell proliferation / antifungal innate immune response ...regulation of mast cell chemotaxis / regulation of cell-substrate adhesion / lymphocyte aggregation / follicular B cell differentiation / inositol trisphosphate biosynthetic process / erythrocyte enucleation / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / positive regulation of mast cell proliferation / antifungal innate immune response / phosphoinositide phospholipase C / regulation of respiratory burst / phosphorylation-dependent protein binding / positive regulation of interleukin-23 production / regulation of neutrophil migration / mast cell proliferation / cellular response to lectin / regulation of mast cell degranulation / positive regulation of cell cycle G1/S phase transition / phospholipid catabolic process / positive regulation of I-kappaB phosphorylation / response to yeast / NADPH oxidase complex / regulation of hydrogen peroxide metabolic process / Toll Like Receptor 4 (TLR4) Cascade / cell activation / positive regulation of neuroinflammatory response / positive regulation of phagocytosis, engulfment / respiratory burst / protein kinase regulator activity / programmed cell death / phosphatidylinositol phospholipase C activity / Erythropoietin activates Phospholipase C gamma (PLCG) / phospholipase C activity / macrophage activation involved in immune response / phosphatidylinositol biosynthetic process / ROS and RNS production in phagocytes / cell projection assembly / phosphatidylinositol-mediated signaling / PCP/CE pathway / cellular response to lipid / positive regulation of neutrophil chemotaxis / negative regulation of programmed cell death / positive regulation of macrophage cytokine production / regulation of canonical NF-kappaB signal transduction / positive regulation of protein targeting to mitochondrion / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / small GTPase-mediated signal transduction / intracellular vesicle / regulation of T cell proliferation / positive regulation of epithelial cell migration / Dectin-2 family / Synthesis of IP3 and IP4 in the cytosol / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / positive regulation of interleukin-10 production / positive regulation of receptor internalization / Generation of second messenger molecules / regulation of lipid metabolic process / RHO GTPases Activate NADPH Oxidases / positive regulation of type I interferon production / response to axon injury / RAC2 GTPase cycle / Role of phospholipids in phagocytosis / positive regulation of calcium-mediated signaling / positive regulation of lamellipodium assembly / regulation of cell migration / release of sequestered calcium ion into cytosol / bone resorption / lipopolysaccharide-mediated signaling pathway / GPVI-mediated activation cascade / protein tyrosine kinase binding / cellular response to calcium ion / positive regulation of interleukin-2 production / positive regulation of interleukin-12 production / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / calcium-mediated signaling / FCERI mediated MAPK activation / B cell receptor signaling pathway / ruffle membrane / CLEC7A (Dectin-1) signaling / platelet activation / Wnt signaling pathway / positive regulation of interleukin-6 production / phagocytic vesicle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by CSF1 (M-CSF) in myeloid cells / positive regulation of DNA-binding transcription factor activity / chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / DAP12 signaling
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / Pleckstrin homology domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / Pleckstrin homology domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Small GTPase Rho / small GTPase Rho family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / SH3 domain / Small GTPase / Ras family / Rab subfamily of small GTPases / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-related C3 botulinum toxin substrate 2 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.4Dec 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA-2
D: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1818
Polymers69,0544
Non-polymers1,1274
Water66737
1
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
D: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0774
Polymers34,5132
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8.8 kcal/mol
Surface area16580 Å2
MethodPQS
2
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
C: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1054
Polymers34,5412
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9.8 kcal/mol
Surface area16620 Å2
MethodPQS
Unit cell
Length a, b, c (Å)131.570, 84.459, 74.196
Angle α, β, γ (deg.)90.00, 112.21, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:20 OR RESSEQ 23:44 OR RESSEQ 51:176 )
211CHAIN B AND (RESSEQ 2:20 OR RESSEQ 23:44 OR RESSEQ 51:176 )
112CHAIN C AND (RESSEQ 7:41 OR RESSEQ 51:85 OR RESSEQ 88:96 OR RESSEQ 98:113 )
212CHAIN D AND (RESSEQ 7:41 OR RESSEQ 51:85 OR RESSEQ 88:96 OR RESSEQ 98:113 )

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 20310.297 Da / Num. of mol.: 2 / 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

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1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA- ... , 2 types, 2 molecules CD

#2: Protein 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA-2 / PHOSPHOINOSITIDE PHOSPHOLIPASE C / PHOSPHOLIPASE C-GAMMA-2 / PLCG2


Mass: 14230.834 Da / Num. of mol.: 1 / Fragment: SPLIT PH DOMAIN, RESIDUES 471-514,841-913
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: P16885, phosphoinositide phospholipase C
#3: Protein 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE GAMMA-2 / PHOSPHOINOSITIDE PHOSPHOLIPASE C / PHOSPHOLIPASE C-GAMMA-2 / PLCG2


Mass: 14202.820 Da / Num. of mol.: 1 / Fragment: SPLIT PH DOMAIN, RESIDUES 471-514,841-913
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: P16885, phosphoinositide phospholipase C

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Non-polymers , 3 types, 41 molecules

#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 12 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLY 12 TO VAL
Sequence detailsTHERE IS A LEADING LINKER SEQUENCE GGGSGGS (NOT SEEN IN STRUCTURE) AND G12V MUTATION THERE IS A ...THERE IS A LEADING LINKER SEQUENCE GGGSGGS (NOT SEEN IN STRUCTURE) AND G12V MUTATION THERE IS A LEADING LINKER SEQUENCE GGGSGGS (NOT SEEN IN STRUCTURE) AND TWO SH2 DOMAINS EXCISED FROM SEQUENCE AND CHAIN REJOINED.

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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: 2.65 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7
Details: RAC2(2-177)GTPGS-PLCSPPH(Y495F) COMPLEX WAS CRYSTALLIZED USING A PROTEIN CONCENTRATION OF 25 MG/ML WITH PRECIPITANT (18% PEG1500, 10% GLYCEROL, 100MM SPG PH9) BY MICRO-SEEDING AT A CONSTANT TEMPERATURE OF 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→70 Å / Num. obs: 29046 / % possible obs: 86.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / % possible all: 52.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UPQ AND 2OVJ

1upq

2ovj


Resolution: 2.3→69.406 Å / SU ML: 0.47 / σ(F): 1.1 / Phase error: 40.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2944 2769 5.1 %
Rwork0.234 --
obs0.237 54867 83.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.445 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 64.77 Å2
Baniso -1Baniso -2Baniso -3
1--9.3864 Å20 Å2-1.4491 Å2
2--17.0954 Å2-0 Å2
3----7.709 Å2
Refinement stepCycle: LAST / Resolution: 2.3→69.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 66 37 4380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014382
X-RAY DIFFRACTIONf_angle_d1.4065959
X-RAY DIFFRACTIONf_dihedral_angle_d18.7361484
X-RAY DIFFRACTIONf_chiral_restr0.095697
X-RAY DIFFRACTIONf_plane_restr0.007741
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1213X-RAY DIFFRACTIONPOSITIONAL
12B1213X-RAY DIFFRACTIONPOSITIONAL0.094
21C733X-RAY DIFFRACTIONPOSITIONAL
22D733X-RAY DIFFRACTIONPOSITIONAL0.11
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33970.3855800.34381302X-RAY DIFFRACTION42
2.3397-2.38230.3749860.34441546X-RAY DIFFRACTION50
2.3823-2.42810.4157880.33641737X-RAY DIFFRACTION55
2.4281-2.47760.4097970.32691920X-RAY DIFFRACTION61
2.4776-2.53150.38561190.35292152X-RAY DIFFRACTION69
2.5315-2.59040.3991130.35362538X-RAY DIFFRACTION81
2.5904-2.65520.42721640.34992931X-RAY DIFFRACTION94
2.6552-2.7270.48191420.3582961X-RAY DIFFRACTION94
2.727-2.80720.4361660.3342972X-RAY DIFFRACTION95
2.8072-2.89780.37931450.28362959X-RAY DIFFRACTION95
2.8978-3.00140.33681840.28212964X-RAY DIFFRACTION95
3.0014-3.12160.40331720.25812968X-RAY DIFFRACTION95
3.1216-3.26370.3591420.24672964X-RAY DIFFRACTION95
3.2637-3.43570.27631380.21042979X-RAY DIFFRACTION95
3.4357-3.6510.27211750.22342959X-RAY DIFFRACTION95
3.651-3.93280.2611320.19972990X-RAY DIFFRACTION95
3.9328-4.32860.2321840.18072958X-RAY DIFFRACTION95
4.3286-4.95480.19881720.1492933X-RAY DIFFRACTION94
4.9548-6.24180.21551550.17692870X-RAY DIFFRACTION93
6.2418-69.43780.22591150.20072495X-RAY DIFFRACTION79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7351-0.5386-0.96391.9770.67832.4159-0.02930.0329-0.0192-0.0886-0.1099-0.1734-0.2566-0.31470.00910.09950.1057-0.03560.02290.02190.13633.67633.05046.2808
29.02693.74283.72642.2420.77680.00140.2621-0.8905-0.12710.0797-0.2451-0.10180.1002-0.1747-0.05710.2149-0.09470.06360.4908-0.02150.276364.065-0.398-17.4463
32.2548-0.64420.09681.8893-0.57230.5513-0.10910.37370.012-0.03250.0726-0.02980.0677-0.4746-0.03630.25390.0340.00470.47370.06660.174233.09770.7523-27.1112
43.7581-0.4579-0.86071.0953-0.09960.7050.15040.85370.2409-0.0797-0.13220.08520.0356-0.3568-0.07150.23920.11490.0050.55610.04150.22134.697710.545219.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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