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- PDB-4k2p: The Structure of a Quintuple Mutant of the Tiam1 PH-CC-Ex Domain -

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Basic information

Entry
Database: PDB / ID: 4k2p
TitleThe Structure of a Quintuple 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


regulation of dopaminergic neuron differentiation / Activated NTRK2 signals through CDK5 / non-canonical Wnt signaling pathway / Rac protein signal transduction / regulation of epithelial to mesenchymal transition / positive regulation of axonogenesis / cell-cell contact zone / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / NRAGE signals death through JNK ...regulation of dopaminergic neuron differentiation / Activated NTRK2 signals through CDK5 / non-canonical Wnt signaling pathway / Rac protein signal transduction / regulation of epithelial to mesenchymal transition / positive regulation of axonogenesis / cell-cell contact zone / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / NRAGE signals death through JNK / small GTPase-mediated signal transduction / CDC42 GTPase cycle / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / EPH-ephrin mediated repulsion of cells / RAC3 GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / cell-matrix adhesion / RAC1 GTPase cycle / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / cell junction / kinase binding / cell-cell junction / cell migration / G alpha (12/13) signalling events / protein-containing complex assembly / positive regulation of cell migration / positive regulation of cell population proliferation / synapse / nucleoplasm / 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 / Tiam1 second PH domain-like / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain / Raf-like Ras-binding ...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 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 / PDZ domain / PH domain profile. / 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 TIAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 1
B: T-lymphoma invasion and metastasis-inducing protein 1
C: T-lymphoma invasion and metastasis-inducing protein 1
D: T-lymphoma invasion and metastasis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8569
Polymers124,6554
Non-polymers2005
Water13,493749
1
A: T-lymphoma invasion and metastasis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2443
Polymers31,1641
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-lymphoma invasion and metastasis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2042
Polymers31,1641
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: T-lymphoma invasion and metastasis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2042
Polymers31,1641
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: T-lymphoma invasion and metastasis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2042
Polymers31,1641
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.507, 70.111, 87.753
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments: (Selection details: chain 'D' and segid 'A' RESTRAINED TORSIONS: 4462 Histogram of...)

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Components

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


Mass: 31163.852 Da / Num. of mol.: 4 / Fragment: PH-CC-Ex domain (UNP residues 429-702) / Mutation: K596A, K597A, K598A, M580L, M586L
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris, 19% 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: Apr 7, 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: 1.98→19.703 Å / Num. obs: 67495 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 23.61 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.3
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.3 / Num. unique all: 9690 / % possible all: 97.6

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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 3A8P

3a8p


Resolution: 1.98→19.703 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 3300 4.96 %
Rwork0.1917 --
obs0.1938 66467 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→19.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7457 0 5 749 8211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067674
X-RAY DIFFRACTIONf_angle_d0.95510398
X-RAY DIFFRACTIONf_dihedral_angle_d13.6692775
X-RAY DIFFRACTIONf_chiral_restr0.0381157
X-RAY DIFFRACTIONf_plane_restr0.0041291
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDTypeAuth asym-ID
11X-RAY DIFFRACTIONPOSITIONAL
12X-RAY DIFFRACTIONPOSITIONALD
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00830.6045910.62691720X-RAY DIFFRACTION64
2.0083-2.03820.35071180.29432630X-RAY DIFFRACTION98
2.0382-2.070.31051490.26272654X-RAY DIFFRACTION99
2.07-2.10390.29181200.24332647X-RAY DIFFRACTION99
2.1039-2.14020.27481470.22312690X-RAY DIFFRACTION100
2.1402-2.1790.22531400.22152673X-RAY DIFFRACTION100
2.179-2.22090.261350.21412678X-RAY DIFFRACTION100
2.2209-2.26620.25731430.23282612X-RAY DIFFRACTION97
2.2662-2.31540.27051540.20112645X-RAY DIFFRACTION99
2.3154-2.36910.31271270.20942720X-RAY DIFFRACTION100
2.3691-2.42830.24721550.20362676X-RAY DIFFRACTION100
2.4283-2.49380.25161400.19882656X-RAY DIFFRACTION100
2.4938-2.5670.23621580.20182654X-RAY DIFFRACTION100
2.567-2.64970.23651470.18732678X-RAY DIFFRACTION100
2.6497-2.74420.25371170.20442719X-RAY DIFFRACTION99
2.7442-2.85370.2681330.20172658X-RAY DIFFRACTION100
2.8537-2.98320.24131350.20442715X-RAY DIFFRACTION100
2.9832-3.13990.24341600.1942692X-RAY DIFFRACTION100
3.1399-3.33570.23241480.18122668X-RAY DIFFRACTION100
3.3357-3.59190.23311340.17372677X-RAY DIFFRACTION99
3.5919-3.95070.22341550.15442611X-RAY DIFFRACTION97
3.9507-4.51630.16611420.14312653X-RAY DIFFRACTION98
4.5163-5.66760.15541230.15892707X-RAY DIFFRACTION98
5.6676-19.70370.22081290.17232734X-RAY DIFFRACTION97
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)
15.6696-1.39581.12994.2454-0.87084.38260.2704-0.0401-0.49120.1614-0.18910.0140.352-0.0831-0.01250.1497-0.0846-0.01940.0988-0.00790.188829.08876.58334.2709
27.7104-0.32021.22072.7074-0.42215.61680.1774-0.4324-0.59330.25950.0860.00040.5203-0.2405-0.18480.193-0.0643-0.06050.20170.06710.229421.91527.2661-2.4943
34.90251.00772.86022.85290.12094.1656-0.00450.1443-0.3458-0.09550.15340.08440.2543-0.178-0.12060.18170.015-0.00090.1812-0.00240.216624.485710.9612-1.6478
45.8952-0.3244-3.95013.08942.68057.9706-0.0858-0.39060.29850.23750.07850.0797-0.4833-0.8116-0.03860.19610.094-0.02070.2481-0.03490.231821.041522.01238.7102
58.2045-2.18355.92482.8869-1.80585.8548-0.0553-1.39320.5723-0.027-0.0099-0.13-0.3021-0.10420.14030.2291-0.04750.04280.3971-0.10490.267241.705924.214725.6598
65.21-1.19564.48582.4545-1.88428.0365-0.188-0.18980.1251-0.1710.033-0.0449-0.23970.15680.19970.2035-0.034-0.00250.2138-0.03730.190640.2119.98616.7721
73.3759-2.41843.12267.96882.18066.5557-0.29510.1862-0.19850.11810.1973-0.0635-0.00990.30630.18910.1712-0.03590.01230.26790.04510.181342.191510.49179.1973
84.6544-0.40982.33093.1486-0.42474.87720.245-0.0628-0.2761-0.0742-0.04370.04020.3482-0.075-0.14520.2159-0.0122-0.01450.31410.00050.20912.33219.553632.2827
93.31160.13682.03570.5114-0.27632.2584-0.0765-0.1340.10240.10350.0251-0.0336-0.1436-0.03110.06090.20520.03250.00160.2058-0.04030.1849-10.269520.023315.4697
104.9792-0.4867-1.57482.14530.72434.55360.0746-0.33440.43830.24530.0732-0.0554-0.47820.3665-0.12670.2316-0.0364-0.00490.1773-0.02210.248415.6469-10.134913.2222
114.81082.9244-2.52984.8826-0.96223.53790.1227-0.19720.075-0.0642-0.0386-0.4085-0.43390.6037-0.09220.2032-0.0483-0.00870.2988-0.00610.246521.5913-11.00913.7291
124.3779-0.1664-3.14924.1712-0.00374.67650.04930.52570.2479-0.3370.04470.0846-0.2488-0.463-0.03620.1541-0.0147-0.00760.16670.01070.25468.9991-16.3289.0812
133.3704-0.40971.12552.4982-1.68348.6167-0.2039-0.7806-0.19030.17910.012-0.1770.22930.62380.21890.12560.04990.02030.36440.05410.268919.0344-24.841720.9136
144.1998-1.8651-4.03662.30630.66574.75480.1195-1.0166-0.1315-0.1833-0.0631-0.06930.27210.51910.09920.23560.0111-0.03970.3140.04370.25-1.9256-26.568337.847
156.8476-1.6387-6.15041.81352.36337.9071-0.182-0.278-0.1908-0.10330.00230.0149-0.01330.23540.20650.17980.0118-0.02090.15370.04620.1946-0.1912-22.347128.8674
168.4699-1.4732-0.41668.59840.75036.3906-0.0169-0.03040.33870.08010.1069-0.0604-0.4401-0.1553-0.10890.1611-0.00730.02940.17-0.02610.1238-1.9364-12.954421.4834
172.9742-0.4097-1.82232.20280.33141.10330.13910.51590.2679-0.06590.02070.0679-0.2526-0.7631-0.10270.26270.1097-0.00980.69920.06080.252837.6014-11.80744.6575
183.2879-0.29493.36971.1351.63076.7525-0.09290.21080.1475-0.0165-0.0475-0.03180.4977-1.3320.10480.331-0.19390.06990.9391-0.01620.303434.1727-24.345535.1257
195.44662.4764-5.1862.3834-1.28575.9930.05970.4778-0.14190.1802-0.0586-0.06260.395-0.57170.12470.268-0.0472-0.02780.3161-0.0150.205655.0265-26.61918.2777
204.13060.138-2.86430.61730.55514.9376-0.04050.0784-0.08580.09520.1177-0.05650.2266-0.4274-0.05340.21480.0167-0.03280.26360.00780.203254.0015-19.187229.5568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 433 through 456 )
2X-RAY DIFFRACTION2chain 'A' and (resid 457 through 477 )
3X-RAY DIFFRACTION3chain 'A' and (resid 478 through 531 )
4X-RAY DIFFRACTION4chain 'A' and (resid 532 through 558 )
5X-RAY DIFFRACTION5chain 'A' and (resid 559 through 593 )
6X-RAY DIFFRACTION6chain 'A' and (resid 594 through 644 )
7X-RAY DIFFRACTION7chain 'A' and (resid 645 through 670 )
8X-RAY DIFFRACTION8chain 'B' and (resid 433 through 531 )
9X-RAY DIFFRACTION9chain 'B' and (resid 532 through 670 )
10X-RAY DIFFRACTION10chain 'C' and (resid 433 through 477 )
11X-RAY DIFFRACTION11chain 'C' and (resid 478 through 504 )
12X-RAY DIFFRACTION12chain 'C' and (resid 505 through 531 )
13X-RAY DIFFRACTION13chain 'C' and (resid 532 through 558 )
14X-RAY DIFFRACTION14chain 'C' and (resid 559 through 593 )
15X-RAY DIFFRACTION15chain 'C' and (resid 594 through 644 )
16X-RAY DIFFRACTION16chain 'C' and (resid 645 through 670 )
17X-RAY DIFFRACTION17chain 'D' and (resid 434 through 531 )
18X-RAY DIFFRACTION18chain 'D' and (resid 532 through 558 )
19X-RAY DIFFRACTION19chain 'D' and (resid 559 through 593 )
20X-RAY DIFFRACTION20chain 'D' and (resid 594 through 670 )

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