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- PDB-1vj6: PDZ2 from PTP-BL in complex with the C-terminal ligand from the A... -

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Basic information

Entry
Database: PDB / ID: 1vj6
TitlePDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein
Components
  • Adenomatous polyposis coli protein
  • protein-tyrosine-phosphatase (nonreceptor type 13)
KeywordsHydrolase/Signaling Protein / PDZ / complex / APC / protein-protein interaction / PTP-BL / C-terminus / Hydrolase-Signaling Protein COMPLEX
Function / homology
Function and homology information


negative regulation of odontogenesis / canonical Wnt signaling pathway involved in negative regulation of apoptotic process / canonical Wnt signaling pathway involved in positive regulation of apoptotic process / negative regulation of acinar cell proliferation / axis specification / RND3 GTPase cycle / Apoptotic cleavage of cellular proteins / acinar cell proliferation / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane ...negative regulation of odontogenesis / canonical Wnt signaling pathway involved in negative regulation of apoptotic process / canonical Wnt signaling pathway involved in positive regulation of apoptotic process / negative regulation of acinar cell proliferation / axis specification / RND3 GTPase cycle / Apoptotic cleavage of cellular proteins / acinar cell proliferation / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nitrogen cycle metabolic process / RND2 GTPase cycle / RND1 GTPase cycle / Deactivation of the beta-catenin transactivating complex / Ovarian tumor domain proteases / regulation of epithelial cell differentiation / negative regulation of cell cycle G1/S phase transition / Degradation of beta-catenin by the destruction complex / Synthesis of PIPs at the plasma membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Scrib-APC-beta-catenin complex / proximal/distal pattern formation / negative regulation of epithelial cell proliferation involved in prostate gland development / positive regulation of fibroblast apoptotic process / regulation of epithelial cell migration / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / metaphase/anaphase transition of mitotic cell cycle / positive regulation of protein localization to centrosome / cell projection membrane / regulation of osteoclast differentiation / pattern specification process / negative regulation of epithelial cell apoptotic process / fibroblast migration / negative regulation of microtubule depolymerization / epithelial cell proliferation involved in prostate gland development / beta-catenin destruction complex / microtubule plus-end binding / dorsal/ventral pattern formation / protein kinase regulator activity / regulation of microtubule-based process / endothelial cell proliferation / fibroblast apoptotic process / microtubule depolymerization / epithelial cell apoptotic process / odontogenesis / positive regulation of fibroblast migration / anterior/posterior pattern specification / skin development / regulation of osteoblast differentiation / stem cell population maintenance / muscle cell cellular homeostasis / mitotic spindle assembly checkpoint signaling / negative regulation of endothelial cell proliferation / negative regulation of Wnt signaling pathway / dynein complex binding / microtubule polymerization / regulation of cell differentiation / mitotic cytokinesis / positive regulation of cell division / lateral plasma membrane / somatic stem cell population maintenance / hair follicle development / canonical Wnt signaling pathway / chromosome organization / axonal growth cone / negative regulation of MAPK cascade / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / protein-tyrosine-phosphatase / positive regulation of cell adhesion / axonogenesis / protein tyrosine phosphatase activity / regulation of cell migration / thymus development / epithelial cell proliferation / cell projection / adherens junction / positive regulation of cell differentiation / kidney development / protein catabolic process / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / kinetochore / ruffle membrane / Wnt signaling pathway / negative regulation of epithelial cell proliferation / positive regulation of protein catabolic process / insulin receptor signaling pathway / cell migration / T cell differentiation in thymus / MAPK cascade / lamellipodium / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / microtubule cytoskeleton / growth cone / protease binding / protein-containing complex assembly
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Armadillo/beta-catenin-like repeats / Armadillo / PDZ domain / FERM central domain / Pdz3 Domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Roll / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Adenomatous polyposis coli protein / Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Initial calculations with XPLOR version 3.851, restrained molecular dynamics protocol under a CHARMM22 forcefield.
AuthorsWalma, T. / Vuister, G.W.
CitationJournal: Structure / Year: 2006
Title: Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering.
Authors: Gianni, S. / Walma, T. / Arcovito, A. / Calosci, N. / Bellelli, A. / Engstrom, A. / Travaglini-Allocatelli, C. / Brunori, M. / Jemth, P. / Vuister, G.W.
History
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein-tyrosine-phosphatase (nonreceptor type 13)
B: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)12,1952
Polymers12,1952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein protein-tyrosine-phosphatase (nonreceptor type 13)


Mass: 10858.336 Da / Num. of mol.: 1 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PTP-BL / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q64512, protein-tyrosine-phosphatase
#2: Protein/peptide Adenomatous polyposis coli protein / APC protein / mAPC


Mass: 1336.518 Da / Num. of mol.: 1 / Fragment: C-terminus of APC / Source method: obtained synthetically
Details: This protein has been chemically synthesized. It is present in mouse.
References: UniProt: Q61315

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM PDZ2 protein, U-15N,13C; 3mM APC peptide, unlabelled
Solvent system: 50 mM KH2PO4/K2HPO4 50 mM KCl, pH 6.8, H2O/D2O (95%/5%)
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2003Delaglioprocessing
X-PLOR3.851Brungerrefinement
CHARMM22MacKerellrefinement
RefinementMethod: Initial calculations with XPLOR version 3.851, restrained molecular dynamics protocol under a CHARMM22 forcefield.
Software ordinal: 1
Details: 1470 distance restraints (intra/sequential/medium/long/inter) (529/323/166/378/74), 28 hydrogen bonds, Dihedral angle restraints (phi/psi/chi) (69/72/13)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 35

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