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- PDB-4e3b: Crystal structure of Tax-Interacting Protein-1 (TIP-1) PDZ domain... -

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Basic information

Entry
Database: PDB / ID: 4e3b
TitleCrystal structure of Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to iCAL36-L (ANSRWPTSIL) peptide
Components
  • Tax1-binding protein 3
  • iCAL50 peptide
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / PDZ-peptide complex / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / regulation of Cdc42 protein signal transduction / negative regulation of Wnt signaling pathway / Rho protein signal transduction / beta-catenin binding / Wnt signaling pathway / fibrillar center / actin cytoskeleton / negative regulation of cell population proliferation ...negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / regulation of Cdc42 protein signal transduction / negative regulation of Wnt signaling pathway / Rho protein signal transduction / beta-catenin binding / Wnt signaling pathway / fibrillar center / actin cytoskeleton / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tax1-binding protein 3 / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tax1-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Stereochemical Determinants of C-terminal Specificity in PDZ Peptide-binding Domains: A NOVEL CONTRIBUTION OF THE CARBOXYLATE-BINDING LOOP.
Authors: Amacher, J.F. / Cushing, P.R. / Bahl, C.D. / Beck, T. / Madden, D.R.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tax1-binding protein 3
B: Tax1-binding protein 3
C: iCAL50 peptide
D: iCAL50 peptide


Theoretical massNumber of molelcules
Total (without water)25,0404
Polymers25,0404
Non-polymers00
Water4,864270
1
A: Tax1-binding protein 3
C: iCAL50 peptide


Theoretical massNumber of molelcules
Total (without water)12,5202
Polymers12,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area6310 Å2
MethodPISA
2
B: Tax1-binding protein 3
D: iCAL50 peptide


Theoretical massNumber of molelcules
Total (without water)12,5202
Polymers12,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.074, 33.599, 66.882
Angle α, β, γ (deg.)80.11, 86.88, 89.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tax1-binding protein 3 / TIP-1 / Glutaminase-interacting protein 3 / Tax interaction protein 1


Mass: 11374.917 Da / Num. of mol.: 2 / Fragment: PDZ domain (UNP residues 11-112)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP3, TIP1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: O14907
#2: Protein/peptide iCAL50 peptide


Mass: 1145.289 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% w/v PEG, 0.25 M potassium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 5, 2011
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→19.18 Å / Num. all: 37114 / Num. obs: 34924 / % possible obs: 94.18 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.075 / Rsym value: 0.035 / Net I/σ(I): 17.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.5-1.580.4034.3653370.235189.8
1.59-1.690.2636.8152870.146193.4
1.7-1.820.1639.7847580.098194.3
1.83-20.09215.1747470.06194.9
2.01-2.230.04722.0941560.04195.9
2.24-2.570.03427.2136620.033195.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SFJ

3sfj


Resolution: 1.5→19.179 Å / SU ML: 0.21 / σ(F): 1.99 / σ(I): 4.36 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1759 5.04 %IN THIN SHELLS
Rwork0.1874 ---
obs0.1889 34924 94.18 %-
all-37114 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.548 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.0742 Å20.4553 Å2-0.1124 Å2
2--6.9707 Å20.5806 Å2
3----1.8966 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 270 2006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061758
X-RAY DIFFRACTIONf_angle_d0.9762367
X-RAY DIFFRACTIONf_dihedral_angle_d12.309677
X-RAY DIFFRACTIONf_chiral_restr0.065267
X-RAY DIFFRACTIONf_plane_restr0.004310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54060.3191160.2692307X-RAY DIFFRACTION86
1.5406-1.58590.29791330.24712549X-RAY DIFFRACTION93
1.5859-1.63710.26921240.2172501X-RAY DIFFRACTION93
1.6371-1.69560.24521460.21062563X-RAY DIFFRACTION94
1.6956-1.76340.25751260.19762545X-RAY DIFFRACTION94
1.7634-1.84360.24911440.19722543X-RAY DIFFRACTION94
1.8436-1.94070.22251330.19122606X-RAY DIFFRACTION95
1.9407-2.06220.21871380.18022564X-RAY DIFFRACTION95
2.0622-2.22120.20411450.17772600X-RAY DIFFRACTION96
2.2212-2.44430.21111270.18092612X-RAY DIFFRACTION96
2.4443-2.79710.22891510.19382588X-RAY DIFFRACTION96
2.7971-3.52040.2229960.17872635X-RAY DIFFRACTION96
3.5204-19.18010.17431800.17252552X-RAY DIFFRACTION95
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)
11.92860.0113-0.81031.63110.13731.5144-0.0304-0.1743-0.08510.09660.0081-0.00460.02-0.08020.00680.0736-0.0048-0.01370.06170.00010.07146.12820.52731.127
21.852-0.1793-0.96941.5060.07111.8155-0.01930.15410.0011-0.06170.0049-0.0147-0.01270.04240.01810.0751-0.0044-0.010.0630.00330.07376.35473.77124.0139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 12:113
2X-RAY DIFFRACTION2chain B and resid 12:113

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