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- PDB-1nmv: Solution structure of human Pin1 -

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Basic information

Entry
Database: PDB / ID: 1nmv
TitleSolution structure of human Pin1
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / PPIase domain / WW domain group IV / beta-alpha
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
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / 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. ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Single Sheet / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBayer, E. / Goettsch, S. / Mueller, J.W. / Griewel, B. / Guiberman, E. / Mayr, L. / Bayer, P.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural Analysis of the Mitotic Regulator hPin1 in Solution: INSIGHTS INTO DOMAIN ARCHITECTURE AND SUBSTRATE BINDING.
Authors: Bayer, E. / Goettsch, S. / Mueller, J.W. / Griewel, B. / Guiberman, E. / Mayr, L.M. / Bayer, P.
#1: Journal: Nature / Year: 1996
Title: A human peptidyl-prolyl isomerase essential for regulation of mitosis
Authors: Lu, K.P. / Hannes, S.D. / Hunter, T.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent
Authors: Ranganathan, R. / Lu, K.P. / Hunter, T. / Noel, J.P.
#3: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for phosphoserine-proline recognition by group IV WW domains
Authors: Verdecia, M.A. / Bowman, M.E. / Lu, K.P. / Hunter, T. / Noel, J.P.
History
DepositionJan 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4May 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)18,2711
Polymers18,2711
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 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #3lowest energy

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Components

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


Mass: 18271.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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 NOESY
121HNHA
1313D 13C-separated NOESY
1413D 15N-separated NOESY
3532D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-0.8mM Pin1 U-15N,13C; 50mM phosphate buffer, 1mM DTT, 5mM EDTA, 50-100mM Na sulfate90% H2O/10% D2O
2~0.2mM Pin1 U-15N,13C; 50mM phosphate buffer, 1mM DTT, 5mM EDTA, 50-100mM Na sulfate100% D2O
30.6mM Pin1 U-15N,13C;50mM Tris/HCl buffer, 1mM DTT, 5mM EDTA90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1n.c. 6.6 ambient 300 K
2n.c. 6.6 ambient 300 K
3n.c. 6.6 ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX5002
Bruker AVANCEBrukerAVANCE6003
Bruker AVANCEBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.2Brukerprocessing
AURELIA2.8.11Brukerdata analysis
VNMR6.18Variancollection
CNS1Bruengerrefinement
NDEE1.2Spin-Updata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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