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- PDB-8w11: Structure of human PIN1 covalently derivatized with SuFEx compound -

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Basic information

Entry
Database: PDB / ID: 8w11
TitleStructure of human PIN1 covalently derivatized with SuFEx compound
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / Covalent derivatization SuFEx
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 / 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 / protein targeting to mitochondrion / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / protein peptidyl-prolyl isomerization / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / postsynaptic cytosol / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of GTPase activity / peptidyl-prolyl cis-trans isomerase activity / ciliary basal body / 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 / regulation of protein stability / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / tau protein binding / neuron differentiation / ISG15 antiviral mechanism / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / positive regulation of protein phosphorylation / response to hypoxia / protein stabilization / nuclear speck / 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
: / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLouie, G.V. / Noel, J.P. / Wang, W.-M. / Kelly, J.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Structure of human PIN1 covalently derivatized with SuFEx compound
Authors: Lastname, F.M.
History
DepositionFeb 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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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: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,19311
Polymers37,2212
Non-polymers1,9729
Water4,720262
1
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6456
Polymers18,6111
Non-polymers1,0345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5495
Polymers18,6111
Non-polymers9384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.151, 200.151, 200.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11B-712-

HOH

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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: 18610.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-A1AET / 3-(fluorosulfonyl)-5-[(2-oxo-2H-1-benzopyran-3-yl)carbamoyl]benzoic acid


Mass: 391.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H10FNO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.49 Å3/Da / Density % sol: 72.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 0.1 M sodium HEPES, 1% v/v polyethylene glycol 400
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2022
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→70.76 Å / Num. obs: 34848 / % possible obs: 100 % / Redundancy: 44.2 % / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.033 / Rrim(I) all: 0.234 / Χ2: 0.47 / Net I/σ(I): 23.6 / Num. measured all: 1721393
Reflection shellResolution: 2.2→2.26 Å / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.3 / Num. measured all: 64560 / Num. unique obs: 2987 / Rpim(I) all: 0.368 / Rrim(I) all: 1.603 / Χ2: 0.22 / Net I/σ(I) obs: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.18 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1751 5.03 %
Rwork0.191 --
obs0.1927 34816 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 125 262 2742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072527
X-RAY DIFFRACTIONf_angle_d0.8633379
X-RAY DIFFRACTIONf_dihedral_angle_d15.031995
X-RAY DIFFRACTIONf_chiral_restr0.047329
X-RAY DIFFRACTIONf_plane_restr0.008433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.26911130.2392522X-RAY DIFFRACTION100
2.26-2.330.28011370.24942482X-RAY DIFFRACTION100
2.33-2.40.29041160.23172528X-RAY DIFFRACTION100
2.4-2.490.26241340.22282492X-RAY DIFFRACTION100
2.49-2.590.23471360.21612526X-RAY DIFFRACTION100
2.59-2.70.25641420.20612502X-RAY DIFFRACTION100
2.7-2.850.23271410.20582509X-RAY DIFFRACTION100
2.85-3.020.23421390.20042517X-RAY DIFFRACTION100
3.03-3.260.22481230.192546X-RAY DIFFRACTION100
3.26-3.590.20841300.17242549X-RAY DIFFRACTION100
3.59-4.10.18111480.15492566X-RAY DIFFRACTION100
4.11-5.160.16391470.14772578X-RAY DIFFRACTION100
5.17-47.180.26351450.21912748X-RAY DIFFRACTION100

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