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- PDB-2nz8: N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1 -

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Basic information

Entry
Database: PDB / ID: 2nz8
TitleN-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1
Components
  • ras-related C3 botulinum toxin substrate 1 isoform Rac1
  • triple functional domain protein
KeywordsSIGNALING PROTEIN / CELL CYCLE / Trio / Rac1 / Dbl-family GEF / Rho-family GTPase / DH/PH cassette
Function / homology
Function and homology information


cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium ...cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / Rac protein signal transduction / regulation of hydrogen peroxide metabolic process / engulfment of apoptotic cell / WNT5:FZD7-mediated leishmania damping / superoxide anion generation / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cell projection assembly / respiratory burst / motor neuron axon guidance / ruffle organization / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / regulation of small GTPase mediated signal transduction / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / sphingosine-1-phosphate receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / RHO GTPases activate KTN1 / forebrain development / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / lamellipodium assembly / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / Wnt signaling pathway, planar cell polarity pathway / negative regulation of fat cell differentiation / extrinsic component of membrane / regulation of receptor signaling pathway via JAK-STAT / presynaptic active zone / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / RHOJ GTPase cycle / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / RAC3 GTPase cycle / positive regulation of focal adhesion assembly / RHOA GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate NADPH Oxidases / positive regulation of substrate adhesion-dependent cell spreading / anatomical structure morphogenesis / positive regulation of stress fiber assembly / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / substrate adhesion-dependent cell spreading / positive regulation of lamellipodium assembly / postsynaptic modulation of chemical synaptic transmission / cell-matrix adhesion / RHO GTPases activate IQGAPs / RHO GTPases activate PKNs / GPVI-mediated activation cascade / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / cell projection / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / neuron projection morphogenesis / positive regulation of endothelial cell migration / axon guidance / guanyl-nucleotide exchange factor activity / secretory granule membrane
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / : / SH3-RhoGEF linking unstructured region / Kalirin-like, spectrin repeats / Kalirin, SH3 / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain ...Rho GDP/GTP exchange factor Kalirin/TRIO / : / : / : / SH3-RhoGEF linking unstructured region / Kalirin-like, spectrin repeats / Kalirin, SH3 / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / : / SOS1/NGEF-like PH domain / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Src homology 3 domains / Rab subfamily of small GTPases / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like 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
Triple functional domain protein / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The DH and PH Domains of Trio Coordinately Engage Rho GTPases for their Efficient Activation
Authors: Chhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J.
History
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ras-related C3 botulinum toxin substrate 1 isoform Rac1
B: triple functional domain protein


Theoretical massNumber of molelcules
Total (without water)56,2732
Polymers56,2732
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-11 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.492, 108.558, 53.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2175-

HOH

21B-2221-

HOH

DetailsThere is one biological unit in each assymetric unit (complex between Rac1 and Trio DH/PH)

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Components

#1: Protein ras-related C3 botulinum toxin substrate 1 isoform Rac1 / Ras-related C3 botulinum toxin substrate 1 / p21-Rac1 / Ras-like protein TC25


Mass: 19710.764 Da / Num. of mol.: 1 / Fragment: soluble part (residues 1-177)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63000
#2: Protein triple functional domain protein / PTPRF-interacting protein


Mass: 36561.953 Da / Num. of mol.: 1 / Fragment: N-terminal DH/PH cassette (residues 1226-1535)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIO / Plasmid: pPROEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O75962
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 100 mM sodium cacodylate pH 5.5 to 6.5, 14 to 18% (w/v) PEG 8000, and 300-500 mM calcium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2004
RadiationMonochromator: double crystal Si (220) cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 39574 / Num. obs: 39416 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.069 / Χ2: 1.824 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.53 / Num. unique all: 3903 / Rsym value: 0.524 / Χ2: 1.124 / % possible all: 99.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å31 Å
Translation3 Å31 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE

1nty

1foe


Resolution: 2→19.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.565 / SU ML: 0.111 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1968 5.1 %RANDOM
Rwork0.223 ---
obs0.225 38900 99.61 %-
all-39416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 0 242 3905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223737
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9735043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0785451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69824.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14915696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5851517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022767
X-RAY DIFFRACTIONr_nbd_refined0.190.21729
X-RAY DIFFRACTIONr_nbtor_refined0.30.22539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.214
X-RAY DIFFRACTIONr_mcbond_it0.521.52359
X-RAY DIFFRACTIONr_mcangle_it0.84823679
X-RAY DIFFRACTIONr_scbond_it1.2631584
X-RAY DIFFRACTIONr_scangle_it1.9134.51364
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 129 -
Rwork0.261 2718 -
obs-2847 99.89 %
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)
11.74430.1444-0.80492.44270.23784.6849-0.04960.0714-0.0816-0.33550.0723-0.12130.31950.0851-0.0227-0.1328-0.0171-0.0041-0.19020.0069-0.197148.08532.129-7.1214
22.506-0.0472-0.26733.5037-0.23851.87320.0028-0.19390.05130.33340.0504-0.01880.06790.0635-0.0531-0.1602-0.03940.0117-0.1770-0.242144.310841.100815.5037
330.0993-1.859313.347412.5573-1.669514.3882.9268-1.1897-5.89470.3162-0.0338-0.01822.5485-0.6843-2.8930.2877-0.2386-0.6478-0.02720.31161.207532.252511.864214.9497
41.1617-0.2572-0.46922.30930.52972.3013-0.0079-0.01120.0247-0.06610.03370.19270.0196-0.0923-0.0258-0.0604-0.0114-0.0088-0.08330.0335-0.056841.964637.17424.9849
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1771 - 177
22BB1231 - 14119 - 189
33BB1412 - 1417190 - 195
43BB1423 - 1434201 - 212
53BB1449 - 1497227 - 275
63BB1505 - 1535283 - 313
74A - BC - D2000 - 2241

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