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- PDB-30tp: 14-3-3sigma protein binding to TSC2-wt peptide -

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Basic information

Entry
Database: PDB / ID: 30tp
Title14-3-3sigma protein binding to TSC2-wt peptide
Components
  • 14-3-3 protein sigma
  • TSC2 peptide pS1254 wt
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / peptide-protein interaction / TSC2
Function / homology
Function and homology information


positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / regulation of cell-cell adhesion / establishment of skin barrier / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein localization to plasma membrane ...positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / regulation of cell-cell adhesion / establishment of skin barrier / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein localization to plasma membrane / cAMP/PKA signal transduction / protein export from nucleus / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of protein localization / positive regulation of 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 / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / cadherin binding / protein kinase binding / signal transduction / : / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
Similarity search - Domain/homology
14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPennings, M.A.M. / Brunsveld, L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101098234European Union
CitationJournal: To Be Published
Title: Mechanistic Insights into Molecular Glue Cooperativity: A 14-3-3 Case Study
Authors: Pennings, M.A.M. / Vandenboorn, E.M.F. / Nooren, L. / Ottmann, C. / Brunsveld, L.
History
DepositionMay 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: TSC2 peptide pS1254 wt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,68512
Polymers27,3252
Non-polymers36010
Water4,360242
1
A: 14-3-3 protein sigma
P: TSC2 peptide pS1254 wt
hetero molecules

A: 14-3-3 protein sigma
P: TSC2 peptide pS1254 wt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36924
Polymers54,6494
Non-polymers72020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555x,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)82.65, 112.649, 62.947
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-306-

CA

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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: 26542.914 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 TSC2 peptide pS1254 wt


Mass: 781.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 252 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.6→66.64 Å / Num. obs: 469510 / % possible obs: 88 % / Redundancy: 13.6 % / CC1/2: 1 / Net I/σ(I): 40.5
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 11.2 / Num. unique obs: 1912 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.126)refinement
PDB-REDO8.2refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.801 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.056 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1768 5.138 %RANDOM
Rwork0.1576 32645 --
all0.159 ---
obs-34413 87.986 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0 Å2
2---0.222 Å20 Å2
3----0.379 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 10 242 2161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0161991
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161905
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.8262692
X-RAY DIFFRACTIONr_angle_other_deg0.5121.5674412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7945.256273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33210385
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4341094
X-RAY DIFFRACTIONr_chiral_restr0.0630.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.2270.2418
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.21567
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2976
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0640.21040
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2136
X-RAY DIFFRACTIONr_metal_ion_refined0.1320.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.215
X-RAY DIFFRACTIONr_nbd_other0.1440.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0910.27
X-RAY DIFFRACTIONr_mcbond_it2.2611.708988
X-RAY DIFFRACTIONr_mcbond_other2.2611.708988
X-RAY DIFFRACTIONr_mcangle_it3.353.061236
X-RAY DIFFRACTIONr_mcangle_other3.353.0631237
X-RAY DIFFRACTIONr_scbond_it3.6972.0581003
X-RAY DIFFRACTIONr_scbond_other3.6912.0581003
X-RAY DIFFRACTIONr_scangle_it5.5843.5951447
X-RAY DIFFRACTIONr_scangle_other5.5823.5971448
X-RAY DIFFRACTIONr_lrange_it6.4221.7752379
X-RAY DIFFRACTIONr_lrange_other6.31619.8322314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.161560.14726790.14828350.9830.9871000.129
1.642-1.6860.2131310.15226620.15427930.9730.9861000.134
1.686-1.7350.1851010.15318000.15527110.9780.98670.12170.134
1.735-1.7890.1871380.15424930.15626320.9780.98699.9620.138
1.789-1.8470.1791390.14624300.14825690.9810.9871000.134
1.847-1.9120.199800.15715690.15824480.9760.98567.36110.142
1.912-1.9840.175600.16110750.16123880.9830.98547.52930.148
1.984-2.0650.2261080.16520980.16823010.9740.98495.87140.155
2.065-2.1560.172850.16216480.16222070.9840.98578.52290.154
2.156-2.2610.159940.14616560.14621400.9860.98881.77570.141
2.261-2.3830.141150.13618260.13619920.9870.98997.43980.135
2.383-2.5280.161110.13718200.13819310.9840.9881000.136
2.528-2.7010.189720.14413880.14617990.9770.98781.15620.147
2.701-2.9170.206840.16515970.16816820.9760.98399.94050.17
2.917-3.1940.188720.17114890.17215610.9790.9821000.179
3.194-3.5690.136480.15711720.15714090.9860.98586.58620.167
3.569-4.1170.169490.169260.16112680.9840.98576.89270.176
4.117-5.0320.165590.15610130.15710720.9860.9871000.18
5.032-7.0740.293450.2098120.2138570.9620.9781000.232
7.074-45.8010.192210.1664920.1675150.9710.98199.61160.188

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