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- PDB-1i8h: SOLUTION STRUCTURE OF PIN1 WW DOMAIN COMPLEXED WITH HUMAN TAU PHO... -

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Basic information

Entry
Database: PDB / ID: 1i8h
TitleSOLUTION STRUCTURE OF PIN1 WW DOMAIN COMPLEXED WITH HUMAN TAU PHOSPHOTHREONINE PEPTIDE
Components
  • MICROTUBULE-ASSOCIATED PROTEIN TAU
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1
KeywordsMEMBRANE PROTEIN/ISOMERASE / CYTOSKELETON / NUCLEAR PROTEIN / MEMBRANE PROTEIN-ISOMERASE COMPLEX
Function / homology
Function and homology information


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 / plus-end-directed organelle transport along microtubule / histone-dependent DNA binding ...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 / plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / protein peptidyl-prolyl isomerization / axonal transport / tubulin complex / positive regulation of protein localization to synapse / regulation of mitotic nuclear division / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of chromosome organization / central nervous system neuron development / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / negative regulation of amyloid-beta formation / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / dynactin binding / regulation of microtubule polymerization / cytoskeletal motor activity / apolipoprotein binding / main axon / protein polymerization / axolemma / glial cell projection / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / postsynaptic cytosol / neurofibrillary tangle assembly / positive regulation of axon extension / negative regulation of protein binding / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / Rho protein signal transduction / synapse assembly / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / supramolecular fiber organization / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / nuclear periphery / regulation of microtubule cytoskeleton organization / protein phosphatase 2A binding / regulation of cytokinesis / cellular response to reactive oxygen species / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / Hsp90 protein binding / microglial cell activation / negative regulation of transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / synapse organization / protein homooligomerization / beta-catenin binding / PKR-mediated signaling / negative regulation of protein catabolic process / regulation of synaptic plasticity / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / response to lead ion / ISG15 antiviral mechanism / microtubule cytoskeleton organization / tau protein binding / memory / cytoplasmic ribonucleoprotein granule / positive regulation of protein phosphorylation / neuron differentiation / neuron projection development
Similarity search - Function
: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. ...: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 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
Microtubule-associated protein tau / 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 1.3Oct 27, 2021Group: 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 6, 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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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: MICROTUBULE-ASSOCIATED PROTEIN TAU
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1


Theoretical massNumber of molelcules
Total (without water)5,9282
Polymers5,9282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 MICROTUBULE-ASSOCIATED PROTEIN TAU / PHF-TAU


Mass: 1464.623 Da / Num. of mol.: 1 / Fragment: (RESIDUES 541-553) / Source method: obtained synthetically
Details: The ligand phosphopeptide was synthesized from Rink amide resin using Fmoc strategy and activation by HBTU and HOBT in a 431A peptide synthesizer. The sequence of the peptide is naturally ...Details: The ligand phosphopeptide was synthesized from Rink amide resin using Fmoc strategy and activation by HBTU and HOBT in a 431A peptide synthesizer. The sequence of the peptide is naturally found in Homo sapiens (Human).
References: UniProt: P10636
#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 Pin1 WW domain / 11mM tau 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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