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- PDB-5d3x: Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)... -

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Basic information

Entry
Database: PDB / ID: 5d3x
TitleCrystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound
ComponentsPhosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
KeywordsLIPID BINDING PROTEIN / pleckstrin homology domain / beta sandwich / phosphatidylinositol-binding
Function / homology
Function and homology information


regulation of dendrite development / regulation of actin filament polymerization / neutrophil activation / negative regulation of TOR signaling / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOC GTPase cycle / RHOJ GTPase cycle ...regulation of dendrite development / regulation of actin filament polymerization / neutrophil activation / negative regulation of TOR signaling / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / T cell differentiation / RHOG GTPase cycle / protein serine/threonine kinase inhibitor activity / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / actin filament polymerization / neutrophil chemotaxis / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / GTPase activator activity / guanyl-nucleotide exchange factor activity / dendritic shaft / phospholipid binding / G alpha (12/13) signalling events / growth cone / intracellular signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytosol
Similarity search - Function
: / 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 / Dbl homology (DH) domain superfamily ...: / 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 / 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 / PDZ superfamily / PH-like domain superfamily / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / 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: 1.69 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
DepositionAug 6, 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 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5744
Polymers38,5742
Non-polymers1,0002
Water3,999222
1
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7872
Polymers19,2871
Non-polymers5001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7872
Polymers19,2871
Non-polymers5001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.742, 72.179, 81.995
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 B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1TYRTYRchain AAA-2 - 4061 - 165
2METMETchain BBB-2 - 4011 - 160

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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: 19286.953 Da / Num. of mol.: 2 / Fragment: unp residues 245-408
Source method: isolated from a genetically manipulated source
Details: pleckstrin homology domain / 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: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: HEPES, Jeffamine ED-2001 pH 7

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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: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 36150 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.23 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.033 / Rrim(I) all: 0.076 / Χ2: 1.388 / Net I/av σ(I): 27.895 / Net I/σ(I): 10.4 / Num. measured all: 176205
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.69-1.724.80.39217720.8940.1920.4380.839100
1.72-1.754.90.34618060.8990.1670.3870.891100
1.75-1.784.80.29117960.9350.1410.3250.892100
1.78-1.824.90.25217860.9420.1220.2820.914100
1.82-1.864.90.21517970.9610.1040.240.992100
1.86-1.94.90.18618100.9710.090.2081.011100
1.9-1.954.90.15717880.9750.0760.1751.115100
1.95-24.90.13118070.9850.0630.1461.147100
2-2.064.90.11218060.990.0550.1251.15100
2.06-2.134.90.10318110.9890.0490.1141.341100
2.13-2.214.90.09617890.9890.0470.1071.498100
2.21-2.294.90.08818280.990.0430.0991.755100
2.29-2.44.90.08218110.9930.040.0921.608100
2.4-2.524.90.0718060.9940.0340.0791.48199.9
2.52-2.684.90.05918260.9960.0290.0661.34899.3
2.68-2.894.90.05718160.9960.0270.0641.50299.1
2.89-3.184.80.06318110.9960.030.072.27598.4
3.18-3.644.90.05118180.9960.0240.0572.34497.7
3.64-4.594.90.04218120.9970.020.0471.91196.5
4.59-504.80.03818540.9980.0190.0431.69192.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3V

5d3v


Resolution: 1.69→29.961 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1807 5.01 %RANDOM
Rwork0.1756 34293 --
obs0.1775 36100 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.41 Å2 / Biso mean: 19.6916 Å2 / Biso min: 3.1 Å2
Refinement stepCycle: final / Resolution: 1.69→29.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 56 222 2659
Biso mean--36.91 27.29 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112581
X-RAY DIFFRACTIONf_angle_d1.4443510
X-RAY DIFFRACTIONf_chiral_restr0.093382
X-RAY DIFFRACTIONf_plane_restr0.006442
X-RAY DIFFRACTIONf_dihedral_angle_d15.476979
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1116X-RAY DIFFRACTION8.32TORSIONAL
12B1116X-RAY DIFFRACTION8.32TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6892-1.73490.28521240.22152579270398
1.7349-1.78590.26571460.201626232769100
1.7859-1.84360.24481390.182126222761100
1.8436-1.90940.21681260.174626312757100
1.9094-1.98590.22611520.175926102762100
1.9859-2.07620.25511460.171226422788100
2.0762-2.18570.23121310.181126532784100
2.1857-2.32250.21541360.173926592795100
2.3225-2.50180.2381390.17826502789100
2.5018-2.75340.20121260.18172664279099
2.7534-3.15150.20031520.17842654280699
3.1515-3.9690.20921420.16112633277597
3.969-29.96550.17781480.17012673282194

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