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- PDB-8vjf: Human R14A Pin1 covalently bound to inhibitor 158D9 -

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Basic information

Entry
Database: PDB / ID: 8vjf
TitleHuman R14A Pin1 covalently bound to inhibitor 158D9
Components
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
  • inhibitor 158D9
KeywordsISOMERASE/INHIBITOR / Destabilizing Inhibitor / PPIase / Structure-Activity Relationship / Drug Design / ISOMERASE / ISOMERASE-INHIBITOR complex
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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division ...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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / postsynaptic cytosol / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / negative regulation of protein binding / positive regulation of GTPase activity / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / neuron differentiation / positive regulation of canonical Wnt signaling pathway / positive regulation of protein phosphorylation / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / ciliary basal body / 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. ...: / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRodriguez, I. / Blaha, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS107479 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA168517 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA285114 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Targeted degradation of Pin1 by protein-destabilizing compounds.
Authors: Alboreggia, G. / Udompholkul, P. / Rodriguez, I. / Blaha, G. / Pellecchia, M.
History
DepositionJan 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
B: inhibitor 158D9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7397
Polymers18,9702
Non-polymers7695
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-56 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.867, 68.867, 78.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 18467.473 Da / Num. of mol.: 1 / Mutation: R14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide inhibitor 158D9


Mass: 502.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 154 molecules

#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: HEPES-NaOH, BisTris, PEG400, TCEP / PH range: 7.1 - 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.7→47.54 Å / Num. obs: 24276 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 24.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.028 / Net I/σ(I): 25.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1284 / Rpim(I) all: 0.356

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BOSdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.54 Å / SU ML: 0.2184 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 1214 5.03 %
Rwork0.2145 22917 -
obs0.2165 24131 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 83 149 1387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711270
X-RAY DIFFRACTIONf_angle_d0.9351699
X-RAY DIFFRACTIONf_chiral_restr0.0509168
X-RAY DIFFRACTIONf_plane_restr0.0077216
X-RAY DIFFRACTIONf_dihedral_angle_d15.7001481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.29771300.25742559X-RAY DIFFRACTION99.93
1.77-1.850.27991310.22632496X-RAY DIFFRACTION99.96
1.85-1.950.3821400.30872452X-RAY DIFFRACTION97.19
1.95-2.070.26021290.2312538X-RAY DIFFRACTION99.93
2.07-2.230.27071400.21842519X-RAY DIFFRACTION99.55
2.23-2.450.27761300.24882508X-RAY DIFFRACTION98.76
2.45-2.810.26781330.23142557X-RAY DIFFRACTION99.96
2.81-3.530.23561410.21172586X-RAY DIFFRACTION100
3.54-47.540.23141400.17812702X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: 29.5301251689 Å / Origin y: -21.9712913008 Å / Origin z: 11.7247958929 Å
111213212223313233
T0.183714716915 Å2-0.0649012620219 Å20.017316759331 Å2-0.185397769453 Å2-0.00110994696762 Å2--0.138834756348 Å2
L2.54687464037 °2-0.430951869566 °20.74324004895 °2-1.57829666265 °2-0.27843407103 °2--2.81334485038 °2
S0.00230372814715 Å °0.123587168825 Å °-0.000541646241558 Å °-0.0314403293145 Å °0.0446501944381 Å °-0.0252950964746 Å °-0.200538197728 Å °0.217782971972 Å °-0.0518659211239 Å °
Refinement TLS groupSelection details: all

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