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- PDB-4nnm: Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (Y... -

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Basic information

Entry
Database: PDB / ID: 4nnm
TitleTax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (YPTSII) 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: 1.6 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 ...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 / 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 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4886
Polymers26,3044
Non-polymers1842
Water2,954164
1
A: Tax1-binding protein 3
C: TIP-1 PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2443
Polymers13,1522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-4 kcal/mol
Surface area7210 Å2
MethodPISA
2
B: Tax1-binding protein 3
D: TIP-1 PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2443
Polymers13,1522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.009, 35.043, 65.626
Angle α, β, γ (deg.)79.62, 87.61, 90.00
Int Tables number1
Space group name H-MP1
DetailsTIP-1 PDZ domain bound to peptide

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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: 12459.160 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: 692.801 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40% (w/v) polyethylene glycol (PEG) 3350, 0.15 M potassium thiocyanate (KSCN), 0.1 M 2-ethanesulfonic acid (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: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.6→19.308 Å / Num. all: 31186 / Num. obs: 30055 / % possible obs: 96.4 % / Observed criterion σ(F): 4.9 / Observed criterion σ(I): 17.48
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.6-1.693.5751960.395195.4
1.7-1.835.9548322.7195.4
1.84-210.14475512.5196.3
2.01-2.2316.8543817.3196.5
2.24-2.5722.9539225.2197
2.58-3.1431.5533613.6197.5

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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: 3SFJ

3sfj


Resolution: 1.6→19.308 Å / SU ML: 0.24 / Cross valid method: omit peptide density / σ(F): 1.99 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1467 4.88 %In thin shells
Rwork0.2048 ---
obs0.2069 30050 96.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.524 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9851 Å20.2691 Å2-0.9302 Å2
2--3.0359 Å21.8044 Å2
3---1.9492 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 12 164 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071891
X-RAY DIFFRACTIONf_angle_d1.0672546
X-RAY DIFFRACTIONf_dihedral_angle_d15.961736
X-RAY DIFFRACTIONf_chiral_restr0.067290
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.30651360.24872787X-RAY DIFFRACTION95
1.6572-1.72350.27081440.23142816X-RAY DIFFRACTION95
1.7235-1.80190.34121430.23152895X-RAY DIFFRACTION96
1.8019-1.89680.27331530.22042807X-RAY DIFFRACTION96
1.8968-2.01550.24121470.20562870X-RAY DIFFRACTION96
2.0155-2.17090.27881490.19932836X-RAY DIFFRACTION96
2.1709-2.38910.24391410.18562873X-RAY DIFFRACTION97
2.3891-2.73390.2211540.20012907X-RAY DIFFRACTION97
2.7339-3.44130.21421530.19042897X-RAY DIFFRACTION98
3.4413-19.30910.25531470.20882895X-RAY DIFFRACTION98

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