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- PDB-3a8p: Crystal structure of the Tiam2 PHCCEx domain -

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Basic information

Entry
Database: PDB / ID: 3a8p
TitleCrystal structure of the Tiam2 PHCCEx domain
ComponentsT-lymphoma invasion and metastasis-inducing protein 2
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor / Alternative splicing / Cell projection / Coiled coil / Cytoplasm / Guanine-nucleotide releasing factor / Lipoprotein / Myristate / Phosphoprotein
Function / homology
Function and homology information


NRAGE signals death through JNK / RAC1 GTPase cycle / G alpha (12/13) signalling events / positive regulation of axonogenesis / small GTPase-mediated signal transduction / GTPase activator activity / guanyl-nucleotide exchange factor activity / filopodium / lamellipodium / growth cone ...NRAGE signals death through JNK / RAC1 GTPase cycle / G alpha (12/13) signalling events / positive regulation of axonogenesis / small GTPase-mediated signal transduction / GTPase activator activity / guanyl-nucleotide exchange factor activity / filopodium / lamellipodium / growth cone / perikaryon / synapse / membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #680 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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 / Tiam1 second PH domain-like / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / Helix non-globular / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Special / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor TIAM2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: T-lymphoma invasion and metastasis-inducing protein 2
B: T-lymphoma invasion and metastasis-inducing protein 2
C: T-lymphoma invasion and metastasis-inducing protein 2
D: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)119,7034
Polymers119,7034
Non-polymers00
Water6,900383
1
A: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.690, 104.790, 115.970
Angle α, β, γ (deg.)90.00, 80.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
T-lymphoma invasion and metastasis-inducing protein 2 / TIAM-2 / SIF and TIAM1-like exchange factor


Mass: 29925.717 Da / Num. of mol.: 4 / Fragment: PHCCEx domain, residues 500-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tiam2, Kiaa2016, Stef / Plasmid: pGEX6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21RIL / References: UniProt: Q6ZPF3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 8000, 100mM Tris-HCl, 200mM Magnesium chloride, pH 8.5, 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 / Date: May 25, 2007
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: 2.08→50 Å / Num. obs: 64571 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.8 Å2
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 80.6

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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 3A8Q

3a8q


Resolution: 2.1→29.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1845113.44 / 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
Rfree0.253 6404 10.1 %RANDOM
Rwork0.211 ---
obs0.211 63378 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.7651 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.24 Å20 Å2-5.28 Å2
2---8.9 Å20 Å2
3----2.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 0 383 7754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
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: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 1001 10.1 %
Rwork0.284 8957 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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