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- PDB-3a8n: Crystal structure of the Tiam1 PHCCEx domain -

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Basic information

Entry
Database: PDB / ID: 3a8n
TitleCrystal structure of the Tiam1 PHCCEx domain
ComponentsT-lymphoma invasion and metastasis-inducing protein 1
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor / Guanine-nucleotide releasing factor / Lipoprotein / Myristate / Phosphoprotein
Function / homology
Function and homology information


positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / RAC3 GTPase cycle / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / NRAGE signals death through JNK ...positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / RAC3 GTPase cycle / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / NRAGE signals death through JNK / kinocilium / RAC1 GTPase cycle / RHOA GTPase cycle / extrinsic component of postsynaptic density membrane / G alpha (12/13) signalling events / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / NMDA selective glutamate receptor signaling pathway / regulation of postsynapse organization / neuron projection extension / main axon / positive regulation of axonogenesis / small GTPase-mediated signal transduction / regulation of GTPase activity / pericentriolar material / Rac protein signal transduction / ephrin receptor signaling pathway / axonal growth cone / somatodendritic compartment / ephrin receptor binding / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / phospholipid binding / receptor tyrosine kinase binding / ruffle membrane / positive regulation of neuron projection development / cell-cell junction / cell migration / microtubule binding / dendritic spine / postsynaptic density / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / synapse / plasma membrane / cytosol
Similarity search - Function
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 ...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. / PH domain / PH domain profile. / PDZ domain / 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
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor TIAM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsTerawaki, S. / Kitano, K. / Mori, T. / Zhai, Y. / Higuchi, Y. / Itoh, N. / Watanabe, T. / Kaibuchi, K. / Hakoshima, T.
CitationJournal: Embo J. / Year: 2010
Title: The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module
Authors: Terawaki, S. / Kitano, K. / Mori, T. / Zhai, Y. / Higuchi, Y. / Itoh, N. / Watanabe, T. / Kaibuchi, K. / Hakoshima, T.
History
DepositionOct 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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)31,6241
Polymers31,6241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.470, 113.470, 113.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 31623.584 Da / Num. of mol.: 1 / Fragment: PHCCEx domain, residues 429-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tiam1, Tiam-1 / Plasmid: pGEX6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21RIL / References: UniProt: Q60610

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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: 3.34 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4% Jeffamine M-600, 10mM Ferric chloride, 1.5% Glycerol, 100mM Sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 2824 / % possible obs: 98.7 % / Redundancy: 10.9 %
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A8P

3a8p


Resolution: 4.5→49.25 Å / Rfactor Rfree error: 0.024 / Data cutoff high absF: 3875577.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.396 262 9.3 %RANDOM
Rwork0.306 ---
obs0.306 2814 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 317.861 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 107 Å2
Baniso -1Baniso -2Baniso -3
1--35.35 Å20 Å20 Å2
2---35.35 Å20 Å2
3---70.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.76 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.16 Å
Refinement stepCycle: LAST / Resolution: 4.5→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 0 1142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.5→4.78 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 46 10.5 %
Rwork0.363 391 -
obs--96.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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