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- PDB-2rud: Solution structure of the peptidyl prolyl cis-trans isomerase dom... -

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Entry
Database: PDB / ID: 2rud
TitleSolution structure of the peptidyl prolyl cis-trans isomerase domain of C113D mutant human Pin1 with sulfate ion
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / protein/cis-trans-isomerase / PPIase
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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction ...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 / postsynaptic cytosol / 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 / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / nuclear speck / positive regulation of protein phosphorylation / cell cycle / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / Chitinase A; domain 3 ...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 / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / Chitinase A; domain 3 / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsXu, N. / Tamari, Y. / Tochio, N. / Tate, S.
CitationJournal: Biochemistry / Year: 2014
Title: The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif.
Authors: Xu, N. / Tochio, N. / Wang, J. / Tamari, Y. / Uewaki, J. / Utsunomiya-Tate, N. / Igarashi, K. / Shiraki, T. / Kobayashi, N. / Tate, S.
History
DepositionMar 25, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1


Theoretical massNumber of molelcules
Total (without water)13,1341
Polymers13,1341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 13133.677 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 51-163 / Mutation: C113D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CO
1513D HNCA
1613D HN(CO)CA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D C(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D (H)CCH-COSY
11313D (H)CCH-TOCSY
11413D HBHA(CO)NH

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Sample preparation

DetailsContents: 0.8 mM [U-13C; U-15N] C113D mutant hPin1 PPIase domain-1, 100 mM sodium sulfate-2, 50 mM sodium phosphate-3, 5 mM EDTA-4, 1 mM DTT-5, 0.03 % sodium azide-6, H2O
Solvent system: 94.12% H2O, 5.88% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMC113D mutant hPin1 PPIase domain-1[U-13C; U-15N]1
100 mMsodium sulfate-21
50 mMsodium phosphate-31
5 mMEDTA-41
1 mMDTT-51
0.03 %sodium azide-61
Sample conditionsIonic strength: 100 / pH: 6.6 / Pressure: ambient / Temperature: 299 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
MAGROkobayashidata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10 / Representative conformer: 1

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