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- PDB-5fi1: Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42 -

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Basic information

Entry
Database: PDB / ID: 5fi1
TitleCrystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42
Components
  • Cell division control protein 42 homolog
  • Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
KeywordsSIGNALING PROTEIN / dbl homology domain / pleckstrin homology domain / GTPase / RhoGEF / PROTEIN BINDING
Function / homology
Function and homology information


GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / regulation of dendrite development / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding ...GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / regulation of dendrite development / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / regulation of actin filament polymerization / neuropilin signaling pathway / establishment of Golgi localization / neutrophil activation / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / negative regulation of TOR signaling / DCC mediated attractive signaling / regulation of postsynapse organization / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / phagocytosis, engulfment / RHOB GTPase cycle / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of mitotic nuclear division / superoxide metabolic process / Myogenesis / heart contraction / establishment of cell polarity / positive regulation of cytokinesis / spindle midzone / RHOC GTPase cycle / RHOJ GTPase cycle / Golgi organization / establishment or maintenance of cell polarity / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / T cell differentiation / RHOG GTPase cycle / protein serine/threonine kinase inhibitor activity / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / actin filament polymerization / neutrophil chemotaxis / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / guanyl-nucleotide exchange factor activity / actin filament organization / dendritic shaft / small monomeric GTPase / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / phospholipid binding / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule
Similarity search - Function
Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / : / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain ...Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / : / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / : / SOS1/NGEF-like PH domain / Small GTPase Rho / Small GTPase Rho domain 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / PDZ superfamily / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / Roll / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog / 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: 3.203 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
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
B: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)64,6842
Polymers64,6842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-19 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.310, 95.906, 277.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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,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.: 1
Source method: isolated from a genetically manipulated source
Details: dbl homology domain/pleckstrin homology domain tandem
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 Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21616.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: pMALc2H10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60953

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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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Ammonium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.16→50 Å / Num. obs: 12403 / % possible obs: 83.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 83.61 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.096 / Net I/av σ(I): 16.062 / Net I/σ(I): 8.3 / Num. measured all: 43371
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.16-3.213.60.4465840.72587.2
3.21-3.273.60.346150.78884.8
3.27-3.343.70.2986390.85882.2
3.34-3.43.70.295850.90384.9
3.4-3.483.60.2156410.91486.9
3.48-3.563.70.2165970.95479
3.56-3.653.70.1596250.99888
3.65-3.753.50.1466190.96784.4
3.75-3.863.50.1176091.0682.4
3.86-3.983.50.1066191.12585.9
3.98-4.123.60.0995981.08179.8
4.12-4.293.40.0856211.13985.3
4.29-4.483.40.0735971.32980.7
4.48-4.723.40.0685971.51778.1
4.72-5.013.30.0666041.49984
5.01-5.43.40.0626031.34279.9
5.4-5.943.50.0586301.27783.2
5.94-6.83.50.0526471.2284.7
6.8-8.563.40.0356581.1984.8
8.56-5030.0297151.19285.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFK, 5D3W

2dfk

5d3w


Resolution: 3.203→43.122 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 622 5.03 %RANDOM
Rwork0.2048 11738 --
obs0.208 12360 81.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.6 Å2 / Biso mean: 124.726 Å2 / Biso min: 61.38 Å2
Refinement stepCycle: final / Resolution: 3.203→43.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 0 0 4194
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034275
X-RAY DIFFRACTIONf_angle_d0.7065781
X-RAY DIFFRACTIONf_chiral_restr0.025658
X-RAY DIFFRACTIONf_plane_restr0.003740
X-RAY DIFFRACTIONf_dihedral_angle_d13.7471612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2026-3.52470.36761300.27072730286077
3.5247-4.03450.29331770.22732951312884
4.0345-5.08170.22411630.20132911307481
5.0817-43.12620.26641520.18083146329884
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)
12.26451.3271-0.96473.1819-0.86862.20730.20080.14610.1117-0.1155-0.21460.0878-0.03760.11520.00010.75530.1994-0.02130.87090.12290.719911.53428.886-16.678
21.3043-0.2987-0.3430.3178-0.35110.7413-0.21790.6907-0.4647-0.7949-0.05410.34151.0241-0.9326-0.00012.293-0.22040.00162.19070.18731.132719.20117.496-60.635
32.4614-0.0665-0.03664.4758-0.12144.67540.36820.5167-0.6992-0.2872-0.2779-0.36560.52490.416100.78250.3019-0.1031.0123-0.06050.913629.22812.801-16.709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 38:244 )A38 - 244
2X-RAY DIFFRACTION2( CHAIN A AND RESID 245:396 )A245 - 396
3X-RAY DIFFRACTION3( CHAIN B AND RESID 0:179 )B0 - 179

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