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- PDB-7bdt: 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1009 -

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Basic information

Entry
Database: PDB / ID: 7bdt
Title14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1009
Components
  • 14-3-3 protein sigma
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPEPTIDE BINDING PROTEIN / 1433 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / regulation of cell-cell adhesion / negative regulation of amyloid-beta formation / cytoskeletal motor activity / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / postsynaptic cytosol / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / negative regulation of protein binding / Rho protein signal transduction / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / regulation of cytokinesis / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / 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 / beta-catenin binding / negative regulation of protein catabolic process / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / tau protein binding / positive regulation of protein phosphorylation / neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / positive regulation of canonical Wnt signaling pathway / regulation of protein localization / regulation of gene expression / positive regulation of cell growth / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / regulation of cell cycle / protein stabilization / nuclear speck / ciliary basal body / cadherin binding / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...: / 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 / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / 14-3-3 protein sigma / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWolter, M. / Dijck, L.v. / Cossar, P.J. / Ottmann, C.
Funding support2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179
H2020 Marie Curie Actions of the European Commission754462
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions.
Authors: Cossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7164
Polymers30,3652
Non-polymers3512
Water6,053336
1
A: 14-3-3 protein sigma
P: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules

A: 14-3-3 protein sigma
P: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4338
Polymers60,7304
Non-polymers7034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4320 Å2
ΔGint-38 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.097, 111.945, 62.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28169.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 2195.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526, peptidylprolyl isomerase
#3: Chemical ChemComp-TJ8 / 2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / LvD1009


Mass: 327.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11BrN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.75→33.971 Å / Num. obs: 26997 / % possible obs: 91.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.785.20.44945768880.8650.2050.4963.356.6
9.09-33.975.10.02312672480.9990.0110.02637.698.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AOG

7aog


Resolution: 1.75→33.971 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 1349 4.99 %
Rwork0.1694 48616 -
obs0.171 26989 91.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.15 Å2 / Biso mean: 17.0574 Å2 / Biso min: 3.9 Å2
Refinement stepCycle: final / Resolution: 1.75→33.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 20 336 2196
Biso mean--23.34 28.41 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072003
X-RAY DIFFRACTIONf_angle_d0.8342718
X-RAY DIFFRACTIONf_chiral_restr0.044294
X-RAY DIFFRACTIONf_plane_restr0.004358
X-RAY DIFFRACTIONf_dihedral_angle_d9.6121634
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7501-1.78370.2498850.2123158654
1.7837-1.82010.25511110.2146220274
1.8201-1.85970.25881070.1994260887
1.8597-1.9030.2421550.2022263790
1.903-1.95050.21121240.1925272191
1.9505-2.00330.21331250.1788271992
2.0033-2.06220.24591800.175267292
2.0622-2.12880.19351510.1666273093
2.1288-2.20480.20031450.1628277293
2.2048-2.29310.21921430.1633284695
2.2931-2.39740.19811590.1647284596
2.3974-2.52380.21311310.1672286796
2.5238-2.68190.24861570.1777283897
2.6819-2.88880.2191260.1778291497
2.8888-3.17930.19151760.1709287398
3.1793-3.63890.18381620.1526292098
3.6389-4.58290.15371570.1427291099
4.5829-33.9710.18321600.1736295699

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