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- PDB-30tr: 14-3-3sigma protein binding to TSC2-weak peptide (AAA mutation) -

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Basic information

Entry
Database: PDB / ID: 30tr
Title14-3-3sigma protein binding to TSC2-weak peptide (AAA mutation)
Components
  • 14-3-3 protein sigma
  • TSC2 peptide pS1254 weak mutant
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: 1.3 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 weak mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4358
Polymers27,2092
Non-polymers2276
Water4,828268
1
A: 14-3-3 protein sigma
P: TSC2 peptide pS1254 weak mutant
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)54,87016
Polymers54,4174
Non-polymers45312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555x,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)82.532, 112.59, 62.819
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

#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 weak mutant


Mass: 665.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
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: 54.13 %
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: Sep 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.3→66.56 Å / Num. obs: 72105 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 1 / Net I/σ(I): 25.4
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3550 / CC1/2: 0.932

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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: 1.3→45.728 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.141 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.148 3675 5.099 %RANDOM
Rwork0.1286 68403 --
all0.13 ---
obs-72078 99.983 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.719 Å2
Baniso -1Baniso -2Baniso -3
1-1.801 Å20 Å2-0 Å2
2---0.576 Å20 Å2
3----1.225 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 6 268 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0162045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161971
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.8272778
X-RAY DIFFRACTIONr_angle_other_deg0.5931.5684564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.235.257292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85210400
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.67910100
X-RAY DIFFRACTIONr_chiral_restr0.0790.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_nbd_refined0.240.2447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21603
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21002
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.21038
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2148
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.250.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.222
X-RAY DIFFRACTIONr_nbd_other0.1410.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1680.29
X-RAY DIFFRACTIONr_mcbond_it4.6031.3011006
X-RAY DIFFRACTIONr_mcbond_other4.5941.3011006
X-RAY DIFFRACTIONr_mcangle_it6.6542.3421263
X-RAY DIFFRACTIONr_mcangle_other6.662.3451264
X-RAY DIFFRACTIONr_scbond_it6.7841.5911039
X-RAY DIFFRACTIONr_scbond_other6.7681.5911039
X-RAY DIFFRACTIONr_scangle_it9.7932.7931497
X-RAY DIFFRACTIONr_scangle_other9.792.7951498
X-RAY DIFFRACTIONr_lrange_it14.86419.2762491
X-RAY DIFFRACTIONr_lrange_other13.16816.8072418
X-RAY DIFFRACTIONr_rigid_bond_restr3.3434016
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
1.3-1.3340.1622870.1450000.14152870.9780.9851000.114
1.334-1.370.1522450.12349090.12451550.9850.98899.98060.1
1.37-1.410.1652450.13247330.13449780.9810.9881000.109
1.41-1.4530.1412360.11346430.11448800.9840.99199.97950.094
1.453-1.5010.1362310.10644760.10747070.9840.9921000.088
1.501-1.5540.1182160.09343420.09445580.9910.9941000.078
1.554-1.6120.1162290.08741950.08944250.9910.99599.97740.074
1.612-1.6780.1362100.08840230.09142340.990.99599.97640.077
1.678-1.7520.1371960.09238820.09440800.9880.99599.9510.081
1.752-1.8380.1432100.09937130.10239230.9870.9941000.089
1.838-1.9370.1441990.10835000.1136990.9870.9931000.099
1.937-2.0540.1461660.11833750.11935410.9860.9921000.11
2.054-2.1960.1351800.11531180.11632980.9910.9921000.11
2.196-2.3710.1321680.11229310.11331000.990.99299.96770.109
2.371-2.5970.1361540.12327220.12328760.9880.9911000.122
2.597-2.9020.171380.14824500.1525890.9810.98799.96140.15
2.902-3.3490.1551300.15921900.15923200.9850.9851000.164
3.349-4.0960.1611070.1518600.15119670.9840.9861000.16
4.096-5.770.165790.16914750.16915540.9870.9861000.189
5.77-45.7280.174490.1978670.1969180.9820.97799.78210.217

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