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- PDB-2kcf: The NMR solution structure of the isolated Apo Pin1 WW domain -

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Basic information

Entry
Database: PDB / ID: 2kcf
TitleThe NMR solution structure of the isolated Apo Pin1 WW domain
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / peptidylprolyl isomerase / Pin1 / WW domain / Cell cycle / Nucleus / Phosphoprotein / Rotamase
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 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...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
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsKowalski, J.A. / Liu, K. / Kelly, J.W.
CitationJournal: Biopolymers / Year: 2002
Title: NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1
Authors: Kowalski, J.A. / Liu, K. / Kelly, J.W.
History
DepositionDec 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_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_ref_seq_dif.details
Revision 1.3May 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: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1


Theoretical massNumber of molelcules
Total (without water)4,1751
Polymers4,1751
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)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4174.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1
Plasmid details: Plasmid contained the sequence of the Pin1 WW domain fused through a thrombin cleavage sequence (Leu-Val-Pro-Arg-Gly-Ser) to the C-terminus of N-terminally His tagged glutathione S- ...Plasmid details: Plasmid contained the sequence of the Pin1 WW domain fused through a thrombin cleavage sequence (Leu-Val-Pro-Arg-Gly-Ser) to the C-terminus of N-terminally His tagged glutathione S-transferase (GST). The expressed protein had the following overall block structure: (His tag)-(GST)-(LVPRGS)-(Pin1 WW domain). Cleavage of the fusion protein with thrombin yielded GS-(Pin1 WW domain)
Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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 DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1mM PIN1, 50 mM potassium phosphate-2, 0.02% v/v sodium azide-3, trace % DSS-4, 90% H2O/10% D2O90% H2O/10% D2O
2mM PIN1, 50 mM potassium phosphate-6, 0.02% v/v sodium azide-7, trace % DSS-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMentity-11.0-1.21
50 mMpotassium phosphate-21
0.02 v/vsodium azide-31
%DSS-41
mMentity-51.0-1.22
50 mMpotassium phosphate-62
0.02 v/vsodium azide-72
%DSS-82
Sample conditionsIonic strength: 0 / pH: 6.2 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DMXBrukerDMX7502
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
PROSAGuntertprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
AmberOPALCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
DYANAGuntert, Braun and Wuthrichstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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