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- PDB-1pin: PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM HOMO SAPIENS -

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Basic information

Entry
Database: PDB / ID: 1pin
TitlePIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM HOMO SAPIENS
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE
KeywordsISOMERASE / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / ROTAMASE / COMPLEX (ISOMERASE-DIPEPTIDE)
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 / regulation of mitotic nuclear division / postsynaptic cytosol / 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 / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / : / positive regulation of GTPase activity / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / 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 ...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. / Chitinase A; domain 3 / WW domain superfamily / 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
Chem-1PG / ALANINE / PROLINE / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT USING MIRAS DERIVED STRUCTURE / Resolution: 1.35 Å
AuthorsNoel, J.P. / Ranganathan, R. / Hunter, T.
Citation
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.
#1: Journal: Nature / Year: 1996
Title: A Human Peptidyl-Prolyl Isomerase Essential for Regulation of Mitosis
Authors: Lu, K.P. / Hanes, S.D. / Hunter, T.
History
DepositionJun 21, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2013Group: Other
Revision 1.4Feb 26, 2014Group: Other
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0766
Polymers18,2711
Non-polymers8055
Water3,675204
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
hetero molecules

A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,15212
Polymers36,5432
Non-polymers1,61010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1
Unit cell
Length a, b, c (Å)49.000, 49.000, 137.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / PIN1


Mass: 18271.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: USING THE HUMAN GENE, THE PROTEIN WAS OVEREXPRESSED IN ESCHERICHIA COLI. THE GENE FOR HUMAN PIN1 WAS INSERTED INTO THE NCOI/BAMHI SITES OF PLASMID PET28A(+) - NOVAGEN -, TRANSFORMED INTO ...Description: USING THE HUMAN GENE, THE PROTEIN WAS OVEREXPRESSED IN ESCHERICHIA COLI. THE GENE FOR HUMAN PIN1 WAS INSERTED INTO THE NCOI/BAMHI SITES OF PLASMID PET28A(+) - NOVAGEN -, TRANSFORMED INTO E. COLI BL21(DE3), AND EXPRESSED AT 20 DEGREES CELSIUS AS A 6HIS N-TERMINAL FUSION PROTEIN. FOLLOWING PURIFICATION USING A NI-NTA RESIN, THE 6HIS FUSION WAS REMOVED BY THROMBIN DIGESTION.
Cell line: HELA CELL / Gene: PIN1 / Plasmid: PET28A(+) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q13526, peptidylprolyl isomerase

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRESIDUES 201 AND 202 WITH FORMS A DIPEPTIDE (ALA-PRO) THAT IS BOUND TO THE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 277 K / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED AT 4 DEGREES CELSIUS FROM 2.4 M (NH4)2SO4, 1% (V/V) PEG 400, 0.1 M NA-HEPES, PH 7.5. PRIOR TO DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO SOLUTIONS OF 40 % ...Details: PROTEIN WAS CRYSTALLIZED AT 4 DEGREES CELSIUS FROM 2.4 M (NH4)2SO4, 1% (V/V) PEG 400, 0.1 M NA-HEPES, PH 7.5. PRIOR TO DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO SOLUTIONS OF 40 % (V/V) PEG 400, 0.1 M NA-HEPES, PH 7.5 CONTAINING 0.05 M ALANINE-PROLINE DIPEPTIDE., temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
22.00-2.50 Mammonium sulfate1reservoir
3100 mMHEPES/Na+1reservoirpH7.5
41 %(v/v)PEG4001reservoir
51 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.35→25 Å / Num. obs: 33672 / % possible obs: 95.5 % / Redundancy: 4.5 % / Rsym value: 0.053 / Net I/σ(I): 18
Reflection shellResolution: 1.35→1.39 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.592 / % possible all: 69
Reflection
*PLUS
Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 69 % / Rmerge(I) obs: 0.592

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT USING MIRAS DERIVED STRUCTURE
Resolution: 1.35→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1 - 5 AND 40 - 44 (WHICH LINK THE WW DOMAIN TO THE PPIASE DOMAIN) WERE NOT VISIBLE IN THE FINAL ELECTRON DENSITY MAP AND SO WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1678 5 %RANDOM
Rwork0.223 ---
obs0.223 31532 95 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 41 204 1458
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it12
X-RAY DIFFRACTIONx_mcangle_it1.51.5
X-RAY DIFFRACTIONx_scbond_it22.5
X-RAY DIFFRACTIONx_scangle_it22
LS refinement shellResolution: 1.35→1.39 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.372 106 5 %
Rwork0.377 2054 -
obs--69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27

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