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- PDB-6vaj: Crystal Structure Analysis of human PIN1 -

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Basic information

Entry
Database: PDB / ID: 6vaj
TitleCrystal Structure Analysis of human PIN1
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE/ISOMERASE INHIBITOR / PPIase / covalent inhibitor / ISOMERASE / 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 / 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
: / 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
Chem-QT7 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Sulfopin is a covalent inhibitor of Pin1 that blocks Myc-driven tumors in vivo.
Authors: Dubiella, C. / Pinch, B.J. / Koikawa, K. / Zaidman, D. / Poon, E. / Manz, T.D. / Nabet, B. / He, S. / Resnick, E. / Rogel, A. / Langer, E.M. / Daniel, C.J. / Seo, H.S. / Chen, Y. / Adelmant, ...Authors: Dubiella, C. / Pinch, B.J. / Koikawa, K. / Zaidman, D. / Poon, E. / Manz, T.D. / Nabet, B. / He, S. / Resnick, E. / Rogel, A. / Langer, E.M. / Daniel, C.J. / Seo, H.S. / Chen, Y. / Adelmant, G. / Sharifzadeh, S. / Ficarro, S.B. / Jamin, Y. / Martins da Costa, B. / Zimmerman, M.W. / Lian, X. / Kibe, S. / Kozono, S. / Doctor, Z.M. / Browne, C.M. / Yang, A. / Stoler-Barak, L. / Shah, R.B. / Vangos, N.E. / Geffken, E.A. / Oren, R. / Koide, E. / Sidi, S. / Shulman, Z. / Wang, C. / Marto, J.A. / Dhe-Paganon, S. / Look, T. / Zhou, X.Z. / Lu, K.P. / Sears, R.C. / Chesler, L. / Gray, N.S. / London, N.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 26, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 8, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)20,5125
Polymers19,8441
Non-polymers6684
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.960, 48.960, 137.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 19844.031 Da / Num. of mol.: 1 / Mutation: K77Q, K82Q
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-QT7 / 2-chloro-N-(2,2-dimethylpropyl)-N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetamide


Mass: 281.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20ClNO3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES-7.5, 3.0M ammonium sulfate / PH range: 7.2-8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.42→39.84 Å / Num. obs: 32304 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.79 Å2 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Net I/σ(I): 17.6 / Num. measured all: 200292
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.42-1.446.31.31005415940.641.63799.7
3.85-39.855.845.61018317620.0110.02796.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIN

1pin


Resolution: 1.42→39.836 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20
RfactorNum. reflection% reflection
Rfree0.2143 1576 4.89 %
Rwork0.1923 --
obs0.1933 32262 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.6 Å2 / Biso mean: 31.7863 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: final / Resolution: 1.42→39.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 41 132 1366
Biso mean--54.24 40.23 -
Num. residues----150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.42-1.46590.31381150.33082751100
1.4659-1.51830.30311400.28032749100
1.5183-1.57910.29311190.24292783100
1.5791-1.65090.20991530.20282724100
1.6509-1.7380.2261510.19362762100
1.738-1.84690.21641470.18142754100
1.8469-1.98950.18391580.1842770100
1.9895-2.18960.19831380.1826279099
2.1896-2.50650.20831570.1904278799
2.5065-3.15770.20131550.1954283299
3.1577-39.8360.22231430.1826298497
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)
13.50780.15361.09264.33830.01953.4725-0.16690.02120.43270.0329-0.0226-0.3249-0.44510.2660.07580.2101-0.0595-0.07640.19110.03680.2131-6.4498-8.828411.1084
24.7024-1.536-0.81433.01750.84582.99740.0493-0.3077-0.07360.2314-0.01720.23030.2059-0.44830.08840.2005-0.03920.00980.20140.05870.174-17.8876-26.158811.8018
32.8091-1.1761.56263.7728-1.26062.50670.03510.0126-0.1684-0.1513-0.128-0.22280.40140.21120.08930.26580.03730.02160.16230.050.2133-4.5304-30.8312.1163
41.8888-0.709-0.29352.44040.09122.3225-0.0363-0.1303-0.25990.1385-0.0350.1130.3919-0.14940.06730.2331-0.0509-0.01570.18110.06310.2041-14.0258-27.45411.3051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 49 )A6 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 62 )A50 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 110 )A63 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 163 )A111 - 163

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