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- PDB-4k2o: The Structure of a Triple Mutant of the Tiam1 PH-CC-Ex Domain -

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Basic information

Entry
Database: PDB / ID: 4k2o
TitleThe Structure of a Triple Mutant of the Tiam1 PH-CC-Ex Domain
ComponentsT-lymphoma invasion and metastasis-inducing protein 1
KeywordsSIGNALING PROTEIN / PH and coiled coil domain / phosphoinositide binding / protein-protein interaction / Par-3 / tight junctions
Function / homology
Function and homology information


positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone ...positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / main axon / neuron projection extension / positive regulation of axonogenesis / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / axonal growth cone / RAC1 GTPase cycle / EPHB-mediated forward signaling / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / regulation of ERK1 and ERK2 cascade / response to cocaine / receptor tyrosine kinase binding / ruffle membrane / kinase binding / G alpha (12/13) signalling events / cell-cell junction / cell migration / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / positive regulation of cell migration / neuronal cell body / lipid binding / glutamatergic synapse / synapse / positive regulation of cell population proliferation / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #680 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain ...Helix Hairpins - #680 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding 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. / Helix Hairpins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / Helix non-globular / PDZ domain / PDZ superfamily / Special / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor TIAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJoshi, M. / Gakhar, L. / Fuentes, E.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: High-resolution structure of the Tiam1 PHn-CC-Ex domain.
Authors: Joshi, M. / Gakhar, L. / Fuentes, E.J.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 20, 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: T-lymphoma invasion and metastasis-inducing protein 1


Theoretical massNumber of molelcules
Total (without water)31,1841
Polymers31,1841
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.831, 80.127, 97.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-879-

HOH

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Components

#1: Protein T-lymphoma invasion and metastasis-inducing protein 1 / TIAM-1


Mass: 31183.926 Da / Num. of mol.: 1 / Fragment: PH-CC-Ex domain (UNP residues 429-702) / Mutation: K596A, K597A, K598A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIAM1 / Plasmid details: contains GB1-rTEV fusion / Plasmid: modified pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q13009
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M calcium chloride, 0.1 M Tris, 20% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→36.915 Å / Num. obs: 16074 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 36.32 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2293 / % possible all: 99.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K2P

4k2p


Resolution: 2.15→36.915 Å / SU ML: 0.25 / σ(F): 0.76 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 807 5.01 %
Rwork0.1759 --
obs0.1781 16067 99.47 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→36.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 103 1954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141891
X-RAY DIFFRACTIONf_angle_d1.3492544
X-RAY DIFFRACTIONf_dihedral_angle_d16.699696
X-RAY DIFFRACTIONf_chiral_restr0.075282
X-RAY DIFFRACTIONf_plane_restr0.007318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21940.33821250.25032644X-RAY DIFFRACTION99
2.2194-2.29870.33071240.25322606X-RAY DIFFRACTION99
2.2987-2.39070.28611440.21712584X-RAY DIFFRACTION99
2.3907-2.49950.27571460.20182621X-RAY DIFFRACTION99
2.4995-2.63130.28211500.18982615X-RAY DIFFRACTION100
2.6313-2.79610.23591700.17742602X-RAY DIFFRACTION99
2.7961-3.01180.24331400.18282597X-RAY DIFFRACTION100
3.0118-3.31480.23151150.17552679X-RAY DIFFRACTION100
3.3148-3.7940.22711270.16642615X-RAY DIFFRACTION100
3.794-4.77840.15791350.14462642X-RAY DIFFRACTION100
4.7784-36.92090.18961440.16862640X-RAY DIFFRACTION100

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