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- PDB-4yon: P-Rex1:Rac1 complex -

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Basic information

Entry
Database: PDB / ID: 4yon
TitleP-Rex1:Rac1 complex
Components
  • Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
  • Ras-related C3 botulinum toxin substrate 1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


regulation of signaling / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / regulation of dendrite development / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process ...regulation of signaling / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / regulation of dendrite development / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / neutrophil activation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / regulation of actin filament polymerization / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / RHOB GTPase cycle / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / superoxide metabolic process / Rac protein signal transduction / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / T cell differentiation / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / GTPase activator activity / cell-matrix adhesion / cell chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / dendritic shaft / VEGFR2 mediated vascular permeability
Similarity search - Function
Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Small GTPase Rho / small GTPase Rho family profile. ...Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Small GTPase Rho / small GTPase Rho family profile. / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rab subfamily of small GTPases / PDZ superfamily / Small GTP-binding protein domain / PH-like domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLucato, C.M. / Whisstock, J.C. / Ellisdon, A.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Phosphatidylinositol (3,4,5)-Trisphosphate-dependent Rac Exchanger 1Ras-related C3 Botulinum Toxin Substrate 1 (P-Rex1Rac1) Complex Reveals the Basis of Rac1 Activation in Breast Cancer Cells.
Authors: Lucato, C.M. / Halls, M.L. / Ooms, L.M. / Liu, H.J. / Mitchell, C.A. / Whisstock, J.C. / Ellisdon, A.M.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references / Other
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: diffrn_source / pdbx_audit_support ...diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization ..._diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
B: Ras-related C3 botulinum toxin substrate 1


Theoretical massNumber of molelcules
Total (without water)65,5382
Polymers65,5382
Non-polymers00
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-16 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.510, 111.250, 158.120
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 Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein / PtdIns(3 / 4 / 5)-dependent Rac exchanger 1


Mass: 45641.215 Da / Num. of mol.: 1 / Fragment: UNP residues 1-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREX1, KIAA1415 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TCU6
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 19896.973 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 sodium MES, pH 6.5, 0.2M sodium acetate, 15% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→40.56 Å / Num. obs: 60929 / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.063 / Rsym value: 0.217 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.337 / Mean I/σ(I) obs: 2.1 / Rpim(I) all: 0.404 / Rsym value: 1.397 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2DFK, 3SBD

2dfk

3sbd


Resolution: 1.95→40.56 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 3030 4.98 %
Rwork0.1623 --
obs0.1633 60883 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 0 780 4977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044277
X-RAY DIFFRACTIONf_angle_d0.7945783
X-RAY DIFFRACTIONf_dihedral_angle_d12.1961617
X-RAY DIFFRACTIONf_chiral_restr0.033658
X-RAY DIFFRACTIONf_plane_restr0.004738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98050.28541410.25042611X-RAY DIFFRACTION100
1.9805-2.01290.26411290.22152598X-RAY DIFFRACTION100
2.0129-2.04760.24461410.20252595X-RAY DIFFRACTION100
2.0476-2.08490.20961420.19062604X-RAY DIFFRACTION100
2.0849-2.1250.20661450.192569X-RAY DIFFRACTION100
2.125-2.16840.22521260.18152623X-RAY DIFFRACTION100
2.1684-2.21550.19331380.17742624X-RAY DIFFRACTION100
2.2155-2.2670.17921300.17042604X-RAY DIFFRACTION100
2.267-2.32370.18151360.16292600X-RAY DIFFRACTION100
2.3237-2.38650.20181280.16522629X-RAY DIFFRACTION100
2.3865-2.45680.1961400.16722601X-RAY DIFFRACTION100
2.4568-2.5360.20981250.16092634X-RAY DIFFRACTION100
2.536-2.62670.17221420.16342615X-RAY DIFFRACTION100
2.6267-2.73180.20051320.15732619X-RAY DIFFRACTION100
2.7318-2.85610.19471480.17242607X-RAY DIFFRACTION100
2.8561-3.00660.21271160.16632671X-RAY DIFFRACTION100
3.0066-3.1950.16981320.15832627X-RAY DIFFRACTION100
3.195-3.44150.16751530.14942627X-RAY DIFFRACTION100
3.4415-3.78760.1631400.14282661X-RAY DIFFRACTION100
3.7876-4.33520.1451300.13722683X-RAY DIFFRACTION100
4.3352-5.45970.16181640.13412655X-RAY DIFFRACTION100
5.4597-40.57030.15771520.16382796X-RAY DIFFRACTION100
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)
13.72973.5987-5.56063.9989-5.63118.5253-0.2757-0.4459-0.4003-0.35990.10250.24010.57450.01910.1510.1903-0.0408-0.02180.32060.02530.2245-0.407428.467587.4978
21.16311.2916-1.53593.3064-3.71475.15290.0907-0.06170.13280.0041-0.01580.0625-0.1588-0.0144-0.10410.11430.0171-0.0070.0697-0.02330.13123.827749.269162.1868
32.533-1.5869-0.92556.5242-0.99673.99720.06260.79170.6781-0.5239-0.09560.0831-0.6549-0.08130.02760.3385-0.0178-0.02920.26740.12660.299810.434759.048839.0092
41.29490.6306-0.98941.3771-0.52791.89630.02820.03820.1092-0.07830.05410.0607-0.0843-0.067-0.07860.11910.0262-0.02980.0851-0.0020.12394.528546.757654.2945
52.11190.5018-1.28621.3385-0.95872.10580.0352-0.13990.00560.0768-0.0967-0.0828-0.09280.07550.13050.12990.0016-0.01940.1004-0.01950.09977.180740.371363.9806
61.835-0.12080.5640.677-0.1161.96410.03130.1882-0.1403-0.0553-0.02640.01660.208-0.13110.17980.13140.0013-0.01260.0543-0.01350.13814.625429.961353.8353
75.43520.3031-2.33464.356-1.28982.72320.2705-0.39150.47480.2050.03920.1302-0.86940.1239-0.23390.23640.0167-0.00020.1531-0.06610.158417.435435.229429.9293
82.6117-1.1276-0.39351.6590.54992.21940.06070.0486-0.0158-0.02130.0021-0.0014-0.1834-0.0584-0.0650.09180.00680.00410.0790.00140.094123.671527.298422.0541
94.90482.69972.05087.11521.77564.61970.0857-0.06530.37910.04630.1208-0.5758-0.710.3932-0.09020.2139-0.0190.0310.1152-0.03860.240225.586835.73719.7997
103.0642-2.33441.08452.39660.86837.74180.03290.2964-0.53180.1344-0.12490.14940.6424-0.72070.16650.1433-0.03720.0140.1448-0.01360.224618.824516.656919.2612
113.71191.0237-0.53241.4415-0.54482.4921-0.16980.0502-0.2669-0.10030.1061-0.1110.17370.16380.05570.15080.01690.01850.1371-0.00290.151633.48117.817214.137
126.74584.0811-2.00996.7404-1.38794.86650.2082-0.5345-0.05350.3519-0.16880.36350.0924-0.0919-0.08120.19190.05250.02470.14240.04540.147724.750414.445628.9172
135.13980.8128-0.53344.43650.85131.5785-0.05550.13090.7069-0.08150.0874-0.6211-0.94270.431-0.10430.3339-0.09650.00840.18810.06550.3528.399949.676859.4057
143.7789-1.86292.23427.16195.3948.32570.102-0.2738-0.17880.3537-0.2850.0930.6339-0.00280.13530.1022-0.0045-0.01320.16620.04530.114420.655832.123265.8703
158.199815.30542.69041.61834.0005-0.2475-0.24260.03240.56980.1126-0.17850.626-0.07690.1330.16230.01140.00240.17640.02470.13419.537738.083870.0666
165.53810.672-0.72284.1926-1.11986.4181-0.027-0.46510.10380.37510.12470.1656-0.4643-0.2726-0.11690.17440.0405-0.00190.1463-0.0120.156516.418844.727972.9156
170.5315-1.4485-1.29644.80451.33158.8073-0.3697-0.41992.17610.5795-0.2838-0.6128-1.07391.00640.57870.4624-0.162-0.12210.4846-0.08390.706332.383454.170768.3857
181.59841.4841-0.55061.59590.75737.6309-0.28240.34451.18070.06120.3403-0.7182-1.09210.9799-0.04180.3268-0.0871-0.07820.28150.0460.6329.980452.960464.4226
194.3311.41131.88671.22641.42892.1950.11570.171-0.03090.015-0.1259-0.1130.03990.11950.01210.11690.03460.00130.12350.03930.119119.202636.977955.5312
201.4341-0.05550.53881.0972-0.77373.68410.05490.1359-0.0852-0.0999-0.0627-0.08550.11090.33440.03530.10280.04910.00840.17740.00270.14528.049730.491763.1644
214.9134-4.215-1.73787.9662-2.86116.6449-0.0782-0.4640.31180.3888-0.1333-0.1076-0.25260.13660.22440.2867-0.0204-0.030.35410.0560.193523.500924.22285.0068
223.70322.7433-0.59625.95232.53335.97420.0172-0.3781-0.66850.1851-0.30250.15420.9405-0.23780.13240.36790.0282-0.02320.25360.11760.278923.050116.543978.7458
232.2804-0.5788-0.96681.4174-0.75513.11990.12260.255-0.0087-0.1109-0.1258-0.32830.13410.50550.03330.1420.1140.00010.29770.0220.212936.92128.131666.8267
243.02570.179-1.47821.9676-1.15413.94220.0264-0.14620.27580.1139-0.0506-0.0539-0.24030.44450.04650.1059-0.027-0.04210.20080.01750.15431.393741.063472.3603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 34:47 )A34 - 47
2X-RAY DIFFRACTION2( CHAIN A AND RESID 48:79 )A48 - 79
3X-RAY DIFFRACTION3( CHAIN A AND RESID 80:99 )A80 - 99
4X-RAY DIFFRACTION4( CHAIN A AND RESID 100:180 )A100 - 180
5X-RAY DIFFRACTION5( CHAIN A AND RESID 181:220 )A181 - 220
6X-RAY DIFFRACTION6( CHAIN A AND RESID 221:245 )A221 - 245
7X-RAY DIFFRACTION7( CHAIN A AND RESID 246:258 )A246 - 258
8X-RAY DIFFRACTION8( CHAIN A AND RESID 259:301 )A259 - 301
9X-RAY DIFFRACTION9( CHAIN A AND RESID 302:330 )A302 - 330
10X-RAY DIFFRACTION10( CHAIN A AND RESID 331:337 )A331 - 337
11X-RAY DIFFRACTION11( CHAIN A AND RESID 338:377 )A338 - 377
12X-RAY DIFFRACTION12( CHAIN A AND RESID 378:399 )A378 - 399
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1:7 )B1 - 7
14X-RAY DIFFRACTION14( CHAIN B AND RESID 8:15 )B8 - 15
15X-RAY DIFFRACTION15( CHAIN B AND RESID 16:19 )B16 - 19
16X-RAY DIFFRACTION16( CHAIN B AND RESID 20:41 )B20 - 41
17X-RAY DIFFRACTION17( CHAIN B AND RESID 42:47 )B42 - 47
18X-RAY DIFFRACTION18( CHAIN B AND RESID 48:55 )B48 - 55
19X-RAY DIFFRACTION19( CHAIN B AND RESID 56:77 )B56 - 77
20X-RAY DIFFRACTION20( CHAIN B AND RESID 78:120 )B78 - 120
21X-RAY DIFFRACTION21( CHAIN B AND RESID 121:125 )B121 - 125
22X-RAY DIFFRACTION22( CHAIN B AND RESID 126:136 )B126 - 136
23X-RAY DIFFRACTION23( CHAIN B AND RESID 137:153 )B137 - 153
24X-RAY DIFFRACTION24( CHAIN B AND RESID 154:176 )B154 - 176

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