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- PDB-4qib: Oxidation-Mediated Inhibition of the Peptidyl-Prolyl Isomerase Pin1 -

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Basic information

Entry
Database: PDB / ID: 4qib
TitleOxidation-Mediated Inhibition of the Peptidyl-Prolyl Isomerase Pin1
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / cis-trans isomerization / Oxidation of active site cysteine / cysteine sulfenic-sulfinic acid redox regulation / parvulin
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 amyloid-beta formation ...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 amyloid-beta formation / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / synapse organization / phosphoprotein binding / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / tau protein binding / regulation of protein stability / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / neuron differentiation / 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 / response to hypoxia / protein stabilization / nuclear speck / cell cycle / 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 / 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 / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Chitinase A; domain 3 / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.865 Å
AuthorsInnes, B.T. / Sowole, M.A. / Konermann, L. / Litchfield, D.W. / Brandl, C.J. / Shilton, B.H.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Peroxide-mediated oxidation and inhibition of the peptidyl-prolyl isomerase Pin1.
Authors: Innes, B.T. / Sowole, M.A. / Gyenis, L. / Dubinsky, M. / Konermann, L. / Litchfield, D.W. / Brandl, C.J. / Shilton, B.H.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3796
Polymers17,6411
Non-polymers7395
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.530, 68.530, 79.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 17640.555 Da / Num. of mol.: 1 / Mutation: R14A
Source method: isolated from a genetically manipulated source
Details: Pin1 coding sequence beginning with LPPGW, preceded by GA, which is left from cloning and cleavage; N-terminal sequence GALPPGW...
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Plasmid: pProEX-HTa Pin1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20 mg/mL protein, 2.0 to 2.4 M ammonium sulfate, 1% poly(ethylene glycol) 400, 100 mM Hepes, 10 mM H2O2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→27.791 Å / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 23.1
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 7.5 / Num. unique all: 2445 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1690)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.865→27.791 Å / SU ML: 0.2 / σ(F): 1.68 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 3501 10.17 %Random
Rwork0.1528 ---
all0.156 34475 --
obs0.156 34414 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.865→27.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 44 202 1404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091222
X-RAY DIFFRACTIONf_angle_d1.3361635
X-RAY DIFFRACTIONf_dihedral_angle_d15.261464
X-RAY DIFFRACTIONf_chiral_restr0.051162
X-RAY DIFFRACTIONf_plane_restr0.007209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8645-1.89010.40991050.3537968X-RAY DIFFRACTION77
1.8901-1.91710.21021490.19461232X-RAY DIFFRACTION100
1.9171-1.94570.24951410.17791275X-RAY DIFFRACTION100
1.9457-1.97610.28051450.18181271X-RAY DIFFRACTION100
1.9761-2.00840.22431190.16581256X-RAY DIFFRACTION100
2.0084-2.04310.26691480.1671213X-RAY DIFFRACTION100
2.0431-2.08020.18691370.15951262X-RAY DIFFRACTION100
2.0802-2.12020.19421320.1611212X-RAY DIFFRACTION100
2.1202-2.16350.19171480.15981268X-RAY DIFFRACTION100
2.1635-2.21050.16751470.14821285X-RAY DIFFRACTION100
2.2105-2.26190.19981400.1441188X-RAY DIFFRACTION100
2.2619-2.31840.20471440.14811285X-RAY DIFFRACTION100
2.3184-2.38110.1951440.14991255X-RAY DIFFRACTION100
2.3811-2.45110.13781420.14091255X-RAY DIFFRACTION100
2.4511-2.53020.17811420.13881223X-RAY DIFFRACTION100
2.5302-2.62050.2281500.15091253X-RAY DIFFRACTION100
2.6205-2.72540.16621360.1481226X-RAY DIFFRACTION100
2.7254-2.84930.17111500.15371259X-RAY DIFFRACTION100
2.8493-2.99930.1771390.1561240X-RAY DIFFRACTION100
2.9993-3.1870.18561330.15541254X-RAY DIFFRACTION100
3.187-3.43270.17661410.14711257X-RAY DIFFRACTION100
3.4327-3.77730.17011380.13551243X-RAY DIFFRACTION100
3.7773-4.32220.15971500.12361260X-RAY DIFFRACTION100
4.3222-5.43880.13131360.14061227X-RAY DIFFRACTION100
5.4388-27.7940.2081450.18771246X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.69560.85341.0022.66091.66383.52880.0076-0.28360.54590.0631-0.1761-0.0374-0.2304-0.07130.1850.1116-0.01140.0150.23230.02470.1879-26.703733.2325-19.7432
25.96291.9467-4.07684.8355-1.43153.4230.0446-0.07510.09780.30420.02090.27680.2759-0.7076-0.20010.3402-0.2580.02510.27760.09180.1594-36.69858.6147-22.0581
32.32492.9290.40086.45280.44742.2505-0.0758-0.0164-0.29980.04630.1136-0.27620.5142-0.1182-0.05750.1735-0.0379-0.02370.14610.01960.1686-25.451712.6222-23.6832
41.7389-0.45970.01773.21740.21212.76310.0205-0.0823-0.0015-0.10170.04470.05320.0308-0.4203-0.04790.0986-0.047-0.01480.21320.02040.1098-32.950423.2866-29.0774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 163 )

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