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- PDB-4nnl: Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to F-iCAL36 (A... -

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Basic information

Entry
Database: PDB / ID: 4nnl
TitleTax-Interacting Protein-1 (TIP-1) PDZ domain bound to F-iCAL36 (ANSRFPTSII) peptide
Components
  • TIP-1 PDZ domain
  • Tax1-binding protein 3
KeywordsPROTEIN BINDING / Tax-Interacting Protein-1 / TIP-1 / PDZ / PDZ-peptide
Function / homology
Function and homology information


negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / activation of GTPase activity / negative regulation of Wnt signaling pathway / Rho protein signal transduction / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / negative regulation of cell population proliferation ...negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / activation of GTPase activity / negative regulation of Wnt signaling pathway / Rho protein signal transduction / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / extracellular exosome / plasma membrane / cytosol / cytoplasm
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: To be Published
Title: A CAL Inhibitor with Single-PDZ Specificity Rescues deltaF508-CFTR
Authors: Cushing, P.R. / Amacher, J.F. / Vouilleme, L. / Culatti, S. / Deng, B. / Gerber, S.A. / Boisguerin, P. / Madden, D.R.
History
DepositionNov 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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
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: TIP-1 PDZ domain
D: TIP-1 PDZ domain


Theoretical massNumber of molelcules
Total (without water)25,1654
Polymers25,1654
Non-polymers00
Water4,450247
1
A: Tax1-binding protein 3
C: TIP-1 PDZ domain


Theoretical massNumber of molelcules
Total (without water)12,5822
Polymers12,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area6400 Å2
MethodPISA
2
B: Tax1-binding protein 3
D: TIP-1 PDZ domain


Theoretical massNumber of molelcules
Total (without water)12,5822
Polymers12,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-5 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.898, 33.574, 66.805
Angle α, β, γ (deg.)100.07, 92.90, 90.02
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11476.020 Da / Num. of mol.: 2
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) / References: UniProt: O14907
#2: Protein/peptide TIP-1 PDZ domain


Mass: 1106.253 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 31% (w/v) polyethylene glycol (PEG), 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.0, 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 4, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→19.557 Å / Num. all: 36831 / Num. obs: 35086 / % possible obs: 95.3 % / Observed criterion σ(F): 6.3 / Observed criterion σ(I): 13.57
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.5-1.615.2675600.299193.5
1.62-1.768.13686018.3194.6
1.77-1.9711.89642411.4195.3
1.98-2.2716.7955027.3195.9
2.28-2.7720.2747065.7196.7
2.78-3.8823.2336734.9197.2

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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→19.557 Å / SU ML: 0.18 / Cross valid method: omit peptide density / σ(F): 1.99 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 1775 5.06 %In thin shells
Rwork0.1808 ---
obs0.1818 35077 95.32 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.022 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9795 Å2-1.3559 Å21.0446 Å2
2--8.063 Å2-2.5791 Å2
3----2.0835 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 247 1997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061802
X-RAY DIFFRACTIONf_angle_d0.9962425
X-RAY DIFFRACTIONf_dihedral_angle_d13.117701
X-RAY DIFFRACTIONf_chiral_restr0.069274
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54050.28561190.24132538X-RAY DIFFRACTION93
1.5405-1.58590.25751490.22072533X-RAY DIFFRACTION94
1.5859-1.6370.25941210.21152468X-RAY DIFFRACTION94
1.637-1.69550.22051400.18672550X-RAY DIFFRACTION94
1.6955-1.76330.19921380.17832555X-RAY DIFFRACTION95
1.7633-1.84350.23761340.18232549X-RAY DIFFRACTION95
1.8435-1.94060.23251370.18072576X-RAY DIFFRACTION96
1.9406-2.06210.18441350.18452572X-RAY DIFFRACTION96
2.0621-2.22110.2191400.17452584X-RAY DIFFRACTION96
2.2211-2.44430.20761260.17872612X-RAY DIFFRACTION96
2.4443-2.79710.19241590.18622562X-RAY DIFFRACTION97
2.7971-3.52070.2064990.17042644X-RAY DIFFRACTION97
3.5207-19.55840.17011780.17092559X-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)
10.8466-0.08650.17270.5311-0.09890.6437-0.01180.0795-0.0357-0.0262-0.009-0.01880.0365-0.02770.02030.0733-0.00280.00770.0637-0.00290.070321.447631.62065.7263
20.764-0.14750.13850.61760.38620.661-0.0199-0.08140.03310.04680.01340.02060.05120.04560.00580.0279-0.00250.01140.01870.00060.02212.97931.959-3.119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:87 )A10 - 87
2X-RAY DIFFRACTION2( CHAIN C AND RESID 2:10 )C2 - 10

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