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- PDB-7bgv: 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1012 -

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Basic information

Entry
Database: PDB / ID: 7bgv
Title14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1012
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 / regulation of mitotic nuclear division / postsynaptic cytosol / regulation of epidermal cell 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 / regulation of mitotic nuclear division / postsynaptic cytosol / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of SMAD protein signal transduction / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / regulation of cell-cell adhesion / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / : / protein kinase A signaling / protein sequestering activity / protein export from nucleus / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / release of cytochrome c from mitochondria / positive regulation of GTPase activity / positive regulation of protein export from nucleus / ciliary basal body / regulation of cytokinesis / stem cell proliferation / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / peptidylprolyl isomerase / TP53 Regulates Metabolic Genes / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / regulation of protein phosphorylation / synapse organization / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical Wnt signaling pathway / protein localization / positive regulation of protein binding / regulation of protein localization / midbody / regulation of gene expression / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / regulation of cell cycle / protein stabilization / nuclear speck / cadherin binding / positive regulation of protein phosphorylation / glutamatergic synapse / protein kinase binding / 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 / 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 / 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
3-methoxy-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: 1.683 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
DepositionJan 8, 2021Deposition 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 13, 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)30,8006
Polymers30,4222
Non-polymers3784
Water6,107339
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)61,60012
Polymers60,8444
Non-polymers7568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4900 Å2
ΔGint-60 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.515, 112.532, 62.778
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

CA

21A-406-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 28226.518 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

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Non-polymers , 5 types, 343 molecules

#3: Chemical ChemComp-TLK / 3-methoxy-4-(2-phenylimidazol-1-yl)benzaldehyde


Mass: 278.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
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: Jan 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.68→41.26 Å / Num. obs: 31746 / % possible obs: 94.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.51 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.071 / Rrim(I) all: 0.175 / Net I/σ(I): 5.7
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1012 / CC1/2: 0.681 / Rpim(I) all: 0.482 / Rrim(I) all: 0.751 / % possible all: 61.5

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Processing

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

7aog


Resolution: 1.683→41.257 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 1653 5.21 %
Rwork0.213 30048 -
obs0.2147 31700 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.83 Å2 / Biso mean: 17.1024 Å2 / Biso min: 4.42 Å2
Refinement stepCycle: final / Resolution: 1.683→41.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 23 339 2224
Biso mean--19.33 27.06 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021941
X-RAY DIFFRACTIONf_angle_d0.4432617
X-RAY DIFFRACTIONf_chiral_restr0.031284
X-RAY DIFFRACTIONf_plane_restr0.002339
X-RAY DIFFRACTIONf_dihedral_angle_d6.8341611
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6833-1.73290.31181000.2941173367
1.7329-1.78880.28241450.2688226287
1.7888-1.85270.2811650.2462241194
1.8527-1.92690.2931320.2475255698
1.9269-2.01460.21621220.2162260798
2.0146-2.12080.23471480.2025260799
2.1208-2.25370.25821210.21122653100
2.2537-2.42770.28671480.244261199
2.4277-2.67190.29721210.233263799
2.6719-3.05840.24641490.2138261098
3.0584-3.85290.20871540.1803264799
3.8529-41.2570.21011480.1864271497

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