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- PDB-6vsk: Crystal structure of the P-Rex1 DEP1 domain -

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Basic information

Entry
Database: PDB / ID: 6vsk
TitleCrystal structure of the P-Rex1 DEP1 domain
ComponentsPhosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
KeywordsSIGNALING PROTEIN / DEP domain / P-Rex1 / metastasis / domain-swapped
Function / homology
Function and homology information


regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle ...regulation of signaling / regulation of dendrite development / neutrophil activation / regulation of actin filament polymerization / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / dendritic shaft / phospholipid binding / G alpha (12/13) signalling events / growth cone / positive regulation of cell migration / intracellular signal transduction / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / enzyme binding / plasma membrane / cytosol
Similarity search - Function
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. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / 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. / 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. / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsTesmer, J. / Ravala, S.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA221289 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL122416 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL071818 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding.
Authors: Ravala, S.K. / Hopkins, J.B. / Plescia, C.B. / Allgood, S.R. / Kane, M.A. / Cash, J.N. / Stahelin, R.V. / Tesmer, J.J.G.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein


Theoretical massNumber of molelcules
Total (without water)10,9701
Polymers10,9701
Non-polymers00
Water724
1
A: Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
x 6


Theoretical massNumber of molelcules
Total (without water)65,8186
Polymers65,8186
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area28530 Å2
ΔGint-187 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.152, 103.152, 67.981
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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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: 10969.662 Da / Num. of mol.: 1 / Fragment: P-Rex1DEP1 domain (UNP residues 409-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREX1, KIAA1415 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TCU6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.76 Å3/Da / Density % sol: 74.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES, pH 6.5, 45% w/v poly(acrylic acid sodium salt)2100

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.12→50 Å / Num. obs: 4105 / % possible obs: 99.3 % / Redundancy: 8.4 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.152 / Net I/σ(I): 19
Reflection shellResolution: 3.12→3.17 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 185 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 0.316 / Rrim(I) all: 0.602 / Χ2: 0.194 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O7F

1o7f


Resolution: 3.12→19.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 35.768 / SU ML: 0.261 / SU R Cruickshank DPI: 0.5506 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.551 / ESU R Free: 0.329
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 213 5.2 %RANDOM
Rwork0.1829 ---
obs0.1855 3862 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 185.9 Å2 / Biso mean: 105.74 Å2 / Biso min: 51.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.6 Å2
Refinement stepCycle: final / Resolution: 3.12→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 0 4 754
Biso mean---65.99 -
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013763
X-RAY DIFFRACTIONr_bond_other_d0.0010.017731
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.6371019
X-RAY DIFFRACTIONr_angle_other_deg1.2361.5871697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.487590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83922.72744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90915155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.04155
X-RAY DIFFRACTIONr_chiral_restr0.0650.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02835
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02160
LS refinement shellResolution: 3.12→3.196 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.395 15 -
Rwork0.284 253 -
obs--93.38 %
Refinement TLS params.Method: refined / Origin x: 43.5 Å / Origin y: -27.958 Å / Origin z: -16.536 Å
111213212223313233
T0.1441 Å2-0.0499 Å2-0.0127 Å2-0.3023 Å2-0.0233 Å2--0.0118 Å2
L2.2982 °20.8486 °2-1.3004 °2-4.2989 °2-1.4515 °2--3.8265 °2
S0.0553 Å °-0.0089 Å °-0.0184 Å °0.0958 Å °-0.1781 Å °0.1233 Å °-0.352 Å °-0.3731 Å °0.1228 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A407 - 497
2X-RAY DIFFRACTION1B1 - 4

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