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- PDB-1i8g: SOLUTION STRUCTURE OF PIN1 WW DOMAIN COMPLEXED WITH CDC25 PHOSPHO... -

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Basic information

Entry
Database: PDB / ID: 1i8g
TitleSOLUTION STRUCTURE OF PIN1 WW DOMAIN COMPLEXED WITH CDC25 PHOSPHOTHREONINE PEPTIDE
Components
  • M-PHASE INDUCER PHOSPHATASE 3
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1
KeywordsHYDROLASE/ISOMERASE / CELL DIVISION / NUCLEAR PROTEIN / HYDROLASE-ISOMERASE COMPLEX
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization ...positive regulation of G2/MI transition of meiotic cell cycle / cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / positive regulation of G2/M transition of mitotic cell cycle / postsynaptic cytosol / negative regulation of protein binding / Rho protein signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / regulation of cytokinesis / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / beta-catenin binding / synapse organization / negative regulation of protein catabolic process / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / G2/M transition of mitotic cell cycle / tau protein binding / positive regulation of protein phosphorylation / neuron differentiation / positive regulation of canonical Wnt signaling pathway / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / ciliary basal body / cell division / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
M-phase inducer phosphatase / M-phase inducer phosphatase / : / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / Rhodanese-like domain superfamily / PPIC-type PPIASE domain ...M-phase inducer phosphatase / M-phase inducer phosphatase / : / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / Rhodanese-like domain superfamily / PPIC-type PPIASE domain / Rhodanese-like domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
M-phase inducer phosphatase 3 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsWintjens, R. / Wieruszeski, J.-M. / Drobecq, H. / Lippens, G. / Landrieu, I.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: 1H NMR study on the binding of Pin1 Trp-Trp domain with phosphothreonine peptides.
Authors: Wintjens, R. / Wieruszeski, J.M. / Drobecq, H. / Rousselot-Pailley, P. / Buee, L. / Lippens, G. / Landrieu, I.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Assembly

Deposited unit
A: M-PHASE INDUCER PHOSPHATASE 3
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1


Theoretical massNumber of molelcules
Total (without water)5,6552
Polymers5,6552
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)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide M-PHASE INDUCER PHOSPHATASE 3


Mass: 1192.209 Da / Num. of mol.: 1 / Fragment: RESIDUES 63-72 / Source method: obtained synthetically
Details: The ligand phosphopeptide was synthesized from Rink amide resin using the Fmoc strategy and activation by HBTU and HOBT in a 431A peptide synthesizer. The sequence of the peptide is ...Details: The ligand phosphopeptide was synthesized from Rink amide resin using the Fmoc strategy and activation by HBTU and HOBT in a 431A peptide synthesizer. The sequence of the peptide is naturally found in Xenopus laevis (African clawed frog).
References: UniProt: P30311, protein-tyrosine-phosphatase
#2: Protein/peptide PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1


Mass: 4462.899 Da / Num. of mol.: 1 / Fragment: WW DOMAIN (RESIDUES 6-44) / Source method: obtained synthetically
Details: The Pin1 WW domain was obtained by peptide synthesis using the BOC-benzyl strategy and the HBTU in situ activation protocol on an Applied 430A peptide synthesizer. The sequence of the ...Details: The Pin1 WW domain was obtained by peptide synthesis using the BOC-benzyl strategy and the HBTU in situ activation protocol on an Applied 430A peptide synthesizer. The sequence of the peptide is naturally found in Homo sapiens (Human).
References: UniProt: Q13526, peptidylprolyl isomerase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: sample of 1mM WW domain / 4.5 mM Cdc25 ligand buffer of 50 mM deutered Tris-D2O, pH 6.4, 100 mM NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.4 / Pressure: ambient / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.structure solution
Discover2.98Molecular Simulation Inc.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: hybrid of distance geometry / simulated annealing protocol Minimization procedure using CVFF as force field
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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