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- PDB-5d3y: Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)... -

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Basic information

Entry
Database: PDB / ID: 5d3y
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: 1.95 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 / diffrn_radiation_wavelength / 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
Water4,450247
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)59.686, 72.859, 77.939
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 249 - 399 / Label seq-ID: 8 - 158

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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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
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.: 247 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: Bis Tris, polypropylene glycol P400

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9789 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: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 25181 / % possible obs: 98.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 15.12 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.056 / Rrim(I) all: 0.116 / Χ2: 0.801 / Net I/av σ(I): 10.529 / Net I/σ(I): 4.9 / Num. measured all: 102248
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9840.46212380.9170.2650.5360.63999.9
1.98-2.0240.39812460.9250.2260.460.67199.8
2.02-2.0640.35812640.9330.2040.4140.67499.6
2.06-2.140.30412510.9570.1730.3520.686100
2.1-2.154.10.27212500.9530.1530.3140.72899.6
2.15-2.24.10.24712430.9610.1380.2840.78299.7
2.2-2.254.10.22212390.9680.1260.2570.73199.6
2.25-2.314.10.19612510.9790.110.2260.72999.5
2.31-2.384.10.19512460.9780.1090.2250.72399.5
2.38-2.464.10.16712580.9840.0930.1920.72699.4
2.46-2.544.10.15512710.9830.0870.1790.73399.4
2.54-2.654.10.14312370.9890.0790.1640.75299.4
2.65-2.774.10.13412450.9870.0750.1550.85299.1
2.77-2.914.10.10812690.9910.060.1240.92998.7
2.91-3.094.10.09112450.9920.0510.1050.9599
3.09-3.334.10.06712740.9970.0370.0770.96298.5
3.33-3.674.10.05112690.9980.0280.0580.93998.4
3.67-4.24.10.04312630.9990.0240.050.89997.8
4.2-5.2840.03712810.9980.020.0420.88397
5.28-303.80.04113410.9980.0230.0471.01795.2

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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: 1.95→29.78 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 1283 5.11 %RANDOM
Rwork0.2074 23820 --
obs0.21 25103 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.53 Å2 / Biso mean: 16.7624 Å2 / Biso min: 4.76 Å2
Refinement stepCycle: final / Resolution: 1.95→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 56 247 2525
Biso mean--14.27 23.08 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122342
X-RAY DIFFRACTIONf_angle_d1.5563178
X-RAY DIFFRACTIONf_chiral_restr0.137356
X-RAY DIFFRACTIONf_plane_restr0.006391
X-RAY DIFFRACTIONf_dihedral_angle_d15.011862
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1280X-RAY DIFFRACTION4.312TORSIONAL
12B1280X-RAY DIFFRACTION4.312TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9504-2.02850.3141220.252126342756100
2.0285-2.12080.32331630.23322606276999
2.1208-2.23260.26981390.22862627276699
2.2326-2.37240.25681290.217626482777100
2.3724-2.55550.27271440.22022625276999
2.5555-2.81250.23731330.21992656278999
2.8125-3.2190.23791580.21922628278699
3.219-4.0540.25711530.18042662281598
4.054-29.78360.23241420.17732734287696

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