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- PDB-2n1o: PIN1 WW domain in complex with a phosphorylated CPEB1 derived peptide -

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Basic information

Entry
Database: PDB / ID: 2n1o
TitlePIN1 WW domain in complex with a phosphorylated CPEB1 derived peptide
Components
  • Cytoplasmic polyadenylation element-binding protein 1
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsIsomerase/Translation regulator / WW / Phosphorylation / CPEB1 / PIN1 / Isomerase-Translation regulator complex
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / cis-trans isomerase activity / phosphothreonine residue binding / translation factor activity, RNA binding / negative regulation of cell motility / ubiquitin ligase activator activity / mRNA 3'-UTR AU-rich region binding / regulation of protein localization to nucleus / GTPase activating protein binding / protein targeting to mitochondrion ...regulation of mRNA 3'-end processing / cis-trans isomerase activity / phosphothreonine residue binding / translation factor activity, RNA binding / negative regulation of cell motility / ubiquitin ligase activator activity / mRNA 3'-UTR AU-rich region binding / regulation of protein localization to nucleus / GTPase activating protein binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / 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 / postsynaptic cytosol / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / negative regulation of cytoplasmic translation / negative regulation of protein binding / positive regulation of GTPase activity / mRNA regulatory element binding translation repressor activity / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / mRNA 3'-UTR binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / cellular response to amino acid stimulus / P-body / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / cellular response to insulin stimulus / neuron differentiation / mRNA processing / positive regulation of canonical Wnt signaling pathway / positive regulation of protein phosphorylation / ribosome binding / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / neuron projection / postsynaptic density / protein stabilization / nuclear speck / ciliary basal body / ribonucleoprotein complex / synapse / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic polyadenylation element-binding protein 1, N-terminal / CPEB-1, RNA recognition motif 1 / Cytoplasmic polyadenylation element-binding protein 1 N-terminus / Cytoplasmic polyadenylation element-binding protein, ZZ domain / Cytoplasmic polyadenylation element-binding protein / CEBP, ZZ domain superfamily / Cytoplasmic polyadenylation element-binding protein ZZ domain / RNA recognition motif / : / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site ...Cytoplasmic polyadenylation element-binding protein 1, N-terminal / CPEB-1, RNA recognition motif 1 / Cytoplasmic polyadenylation element-binding protein 1 N-terminus / Cytoplasmic polyadenylation element-binding protein, ZZ domain / Cytoplasmic polyadenylation element-binding protein / CEBP, ZZ domain superfamily / Cytoplasmic polyadenylation element-binding protein ZZ domain / RNA recognition motif / : / 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 / 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 / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Cytoplasmic polyadenylation element-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsSchelhorn, C. / Macias, M. / Martin-Malpartida, P.
CitationJournal: Sci Rep / Year: 2015
Title: Structural Analysis of the Pin1-CPEB1 interaction and its potential role in CPEB1 degradation.
Authors: Schelhorn, C. / Martin-Malpartida, P. / Sunol, D. / Macias, M.J.
History
DepositionApr 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
B: Cytoplasmic polyadenylation element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)4,9082
Polymers4,9082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area667.9 Å2
ΔGint0.7 kcal/mol
Surface area3362.9 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 3901.333 Da / Num. of mol.: 1 / Fragment: UNP residues 7-39
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide Cytoplasmic polyadenylation element-binding protein 1 / CPE-BP1 / CPE-binding protein 1 / h-CPEB / hCPEB-1


Mass: 1007.100 Da / Num. of mol.: 1 / Fragment: UNP residues 206-213 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BZB8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM Pin1, 3 mM CPEB1, 10 % [U-100% 2H] D2O, 20 mM [U-100% 2H] TRIS, 130 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPin1-11
3 mMCPEB1-21
10 %D2O-3[U-100% 2H]1
20 mMTRIS-4[U-100% 2H]1
130 mMsodium chloride-51
Sample conditionspH: 7 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSSOLVErefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 19 / Representative conformer: 1

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