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- PDB-5fi0: Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1 -

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Basic information

Entry
Database: PDB / ID: 5fi0
TitleCrystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1
Components
  • Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
  • Ras-related C3 botulinum toxin substrate 1
KeywordsPROTEIN BINDING / dbl homology domain / pleckstrin homology domain / beta sandwich / small GTPase
Function / homology
Function and homology information


regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / neutrophil activation / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / regulation of small GTPase mediated signal transduction / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / RHOB GTPase cycle / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / RHOC GTPase cycle / regulation of cell size / Rac protein signal transduction / DSCAM interactions / superoxide metabolic process / RHOJ GTPase cycle / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHOQ GTPase cycle / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / RHOA GTPase cycle / positive regulation of focal adhesion assembly / CDC42 GTPase cycle / RHOG GTPase cycle / T cell differentiation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / RAC3 GTPase cycle / RAC2 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / RHO GTPases activate PKNs / localization / regulation of actin cytoskeleton organization / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of microtubule polymerization / G protein activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RAC1 GTPase cycle / neuron migration / actin filament polymerization / GTPase activator activity / small monomeric GTPase / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell motility / actin filament organization / secretory granule membrane / neutrophil chemotaxis / RHO GTPases Activate Formins / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane
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 family profile. / Small GTPase Rho ...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 family profile. / Small GTPase Rho / 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. / Rho (Ras homology) subfamily of Ras-like small GTPases / Pleckstrin homology domain. / Pleckstrin homology domain / Small GTPase / Ras family / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / 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
PHOSPHATE ION / 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 / molecular replacement / Resolution: 3.282 Å
AuthorsCash, J.N. / Tesmer, J.J.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122416 United States
American Cancer SocietyPF-14-224-01-DMC United States
CitationJournal: Structure / Year: 2016
Title: Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3.
Authors: Cash, J.N. / Davis, E.M. / Tesmer, J.J.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
B: Ras-related C3 botulinum toxin substrate 1
C: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
D: Ras-related C3 botulinum toxin substrate 1
E: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
F: Ras-related C3 botulinum toxin substrate 1
G: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
H: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,89212
Polymers259,5128
Non-polymers3804
Water0
1
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
B: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9733
Polymers64,8782
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-16 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
D: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9733
Polymers64,8782
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area25570 Å2
MethodPISA
3
E: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
F: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9733
Polymers64,8782
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-18 kcal/mol
Surface area25860 Å2
MethodPISA
4
G: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
H: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9733
Polymers64,8782
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-18 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.373, 107.053, 323.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
12chain B
22chain D
32chain F
42chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0 - 398
211chain CC38 - 399
311chain EE-2 - 397
411chain GG-2 - 398
112chain BB3 - 178
212chain DD2 - 179
312chain FF1 - 181
412chain HH3 - 181

NCS ensembles :
ID
1
2

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Components

#1: Protein
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein / PtdIns(3 / 4 / 5)-dependent Rac exchanger 1


Mass: 43066.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREX1, KIAA1415 / Plasmid: pMALc2H10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 21811.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Plasmid: pMALc2H10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63000
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

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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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium dihydrogen phosphate, PEG 8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.12721
21.1271
ReflectionResolution: 3.25→35 Å / Num. obs: 42862 / % possible obs: 98 % / Redundancy: 5.8 % / Biso Wilson estimate: 67.13 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.076 / Rrim(I) all: 0.19 / Χ2: 1.484 / Net I/av σ(I): 10.778 / Net I/σ(I): 5.6 / Num. measured all: 247146
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.315.50.8719970.7750.3770.9520.98291.9
3.31-3.375.40.76720210.7860.3340.840.9994
3.37-3.435.50.6420140.8030.280.7011.03895
3.43-3.55.40.53420720.8640.2350.5861.02595.2
3.5-3.585.50.46620520.8840.2060.5121.07596.4
3.58-3.665.40.421200.9180.1780.441.15697.1
3.66-3.755.50.3420930.930.1510.3741.22597.9
3.75-3.855.50.30221110.9540.1360.3331.28898
3.85-3.975.60.26521200.9550.1190.2921.32798.8
3.97-4.095.60.23221490.9670.1050.2551.42999
4.09-4.245.60.20921900.9660.0940.231.58999
4.24-4.415.70.17721400.9730.080.1951.70899.3
4.41-4.615.80.16121520.9790.0720.1771.83999.5
4.61-4.855.80.13721710.9850.0620.1511.90299.3
4.85-5.155.90.1421760.9860.0620.1541.79899.8
5.15-5.556.10.14722030.9840.0640.1611.71199.8
5.55-6.116.40.14922170.9840.0640.1621.773100
6.11-6.996.50.12722280.9910.0530.1382.017100
6.99-8.786.50.09122800.9940.0380.0981.476100
8.78-3560.06623560.9960.0290.0721.7798.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFK and 5D3W

2dfk

5d3w


Resolution: 3.282→34.847 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 2104 4.92 %
Rwork0.1902 40671 -
obs0.1924 42775 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.27 Å2 / Biso mean: 81.2588 Å2 / Biso min: 22.02 Å2
Refinement stepCycle: final / Resolution: 3.282→34.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16711 0 20 0 16731
Biso mean--101.14 --
Num. residues----2089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517048
X-RAY DIFFRACTIONf_angle_d1.04823056
X-RAY DIFFRACTIONf_chiral_restr0.0442614
X-RAY DIFFRACTIONf_plane_restr0.0062945
X-RAY DIFFRACTIONf_dihedral_angle_d15.5686429
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6761X-RAY DIFFRACTION10.134TORSIONAL
12C6761X-RAY DIFFRACTION10.134TORSIONAL
13E6761X-RAY DIFFRACTION10.134TORSIONAL
14G6761X-RAY DIFFRACTION10.134TORSIONAL
21B3390X-RAY DIFFRACTION10.134TORSIONAL
22D3390X-RAY DIFFRACTION10.134TORSIONAL
23F3390X-RAY DIFFRACTION10.134TORSIONAL
24H3390X-RAY DIFFRACTION10.134TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2823-3.35860.24731030.25212139224277
3.3586-3.44260.31651350.25592587272294
3.4426-3.53560.3151270.24162639276695
3.5356-3.63950.28081300.22332637276796
3.6395-3.75680.24181330.21432690282397
3.7568-3.89090.24881440.19692720286498
3.8909-4.04650.23911340.1942739287399
4.0465-4.23040.23121500.18112737288799
4.2304-4.4530.21941340.1652763289799
4.453-4.73130.20941400.162927812921100
4.7313-5.09560.21821530.16222803295699
5.0956-5.60650.23741630.1827722935100
5.6065-6.41340.23551620.205728132975100
6.4134-8.06360.24221460.197428773023100
8.0636-34.84870.20031500.16592974312499
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)
14.32311.5659-0.033.9842-0.93734.0787-0.02460.08650.15480.2332-0.12310.11920.0575-0.30020.16150.24160.0719-0.05940.2582-0.03330.34412.27828.844793.4674
22.074-1.6571-0.54862.8918-0.6122.5007-0.506-0.75250.01790.98980.1074-0.10470.3463-0.19140.35451.253-0.13920.07271.2267-0.01310.57495.05528.3927138.6826
33.1107-0.90350.77993.66-0.20753.63970.13380.0554-0.17190.0249-0.124-0.19540.12450.0788-0.07010.28570.0071-0.09440.26440.00280.323516.40519.445796.6816
43.13671.03330.18765.8333-0.35233.27760.1301-0.1340.1735-0.031-0.0490.90580.2642-0.4239-0.02750.26360.0223-0.13580.32870.01070.55376.1998-25.403292.8411
52.279-1.6017-0.7692.97610.2623.1026-0.7398-0.9929-0.24470.90760.66350.2941-0.12190.1701-0.0571.06670.00820.2091.65170.07120.76715.7831-28.1633138.1471
62.4866-0.5301-0.25223.5168-0.0353.82410.11750.0083-0.1811-0.2137-0.0864-0.14880.4070.3021-0.06140.36260.018-0.160.3540.05090.479723.0801-42.738595.0577
72.8546-0.74370.82953.19870.04755.5169-0.2738-0.38620.42170.58060.0985-0.0999-0.26-0.87340.15890.36840.0995-0.12260.4908-0.07340.392636.1858-1.173119.3713
81.31430.35451.0851.4769-1.15692.07840.4975-1.3088-0.06971.314-0.7053-0.5356-1.17460.33380.30711.8364-0.2998-0.52211.7931-0.04480.841351.9606-3.8412161.0704
94.0823-0.63020.28558.02850.75554.666-0.2095-0.1673-0.63561.03880.15130.18390.5135-0.06780.13620.47910.0469-0.00010.35210.02420.495940.8398-24.9074124.5481
103.6665-0.18260.3824.1452-0.67614.2419-0.1514-0.01460.32310.5083-0.09190.00630.1541-0.13350.2340.52730.1236-0.04680.3548-0.06090.431438.4544-53.3614119.011
112.10320.3603-0.58013.5012-0.64511.6947-0.2313-0.86430.20511.9308-0.3329-0.4381-1.7580.18780.38372.3939-0.1825-0.18621.4113-0.12570.652351.4466-59.2131161.5401
123.8139-1.2936-0.29997.42540.55193.7494-0.2788-0.1331-0.61071.199-0.14970.99640.7043-0.32580.48020.82350.00260.24150.43-0.06930.524240.4859-77.6755122.7682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 244 )A0 - 244
2X-RAY DIFFRACTION2chain 'A' and (resid 245 through 398 )A245 - 398
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 178 )B3 - 178
4X-RAY DIFFRACTION4chain 'C' and (resid 38 through 244 )C38 - 244
5X-RAY DIFFRACTION5chain 'C' and (resid 245 through 399 )C245 - 399
6X-RAY DIFFRACTION6chain 'D' and (resid 2 through 179 )D2 - 179
7X-RAY DIFFRACTION7chain 'E' and (resid -2 through 244 )E-2 - 244
8X-RAY DIFFRACTION8chain 'E' and (resid 245 through 397 )E245 - 397
9X-RAY DIFFRACTION9chain 'F' and (resid 1 through 181 )F1 - 181
10X-RAY DIFFRACTION10chain 'G' and (resid -2 through 244 )G-2 - 244
11X-RAY DIFFRACTION11chain 'G' and (resid 245 through 398 )G245 - 398
12X-RAY DIFFRACTION12chain 'H' and (resid 3 through 181 )H3 - 181

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