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

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Basic information

Entry
Database: PDB / ID: 30ts
Title14-3-3sigma protein binding to TSC2-weak peptide (AAA mutation) and stabilizer 3'deAc FC-A.
Components
  • 14-3-3 protein sigma
  • TSC2 peptide pS1254 weak mutant
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / peptide-protein interaction / TSC2 / stabilizer
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
De-acetylated Fusicoccin / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: TSC2 peptide pS1254 weak mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2276
Polymers27,4682
Non-polymers7594
Water2,846158
1
A: 14-3-3 protein sigma
B: TSC2 peptide pS1254 weak mutant
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,45412
Polymers54,9364
Non-polymers1,5188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.857, 111.922, 62.908
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-545-

HOH

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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: 924.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SIT / De-acetylated Fusicoccin / [(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl] ethanoate


Mass: 638.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H54O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
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: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.7→45.772 Å / Num. obs: 32120 / % possible obs: 99.1 % / Redundancy: 4.5 % / CC1/2: 0.998 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1695 / CC1/2: 0.788

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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: 1.7→45.772 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.857 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1591 4.958 %RANDOM
Rwork0.1693 30499 --
all0.171 ---
obs-32090 98.614 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.513 Å2
Baniso -1Baniso -2Baniso -3
1-1.463 Å20 Å2-0 Å2
2---0.769 Å20 Å2
3----0.694 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 48 158 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0162003
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161903
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.8292709
X-RAY DIFFRACTIONr_angle_other_deg0.5571.5684402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4415.267262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.59558
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.96956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37210364
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3421090
X-RAY DIFFRACTIONr_chiral_restr0.0730.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.2350.2419
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21647
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21017
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2123
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3880.211
X-RAY DIFFRACTIONr_nbd_other0.2310.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0850.21
X-RAY DIFFRACTIONr_mcbond_it4.4662.425986
X-RAY DIFFRACTIONr_mcbond_other4.4412.424986
X-RAY DIFFRACTIONr_mcangle_it5.8124.331230
X-RAY DIFFRACTIONr_mcangle_other5.814.3321231
X-RAY DIFFRACTIONr_scbond_it6.5442.951017
X-RAY DIFFRACTIONr_scbond_other6.5442.951017
X-RAY DIFFRACTIONr_scangle_it9.0745.0771477
X-RAY DIFFRACTIONr_scangle_other9.0715.0781478
X-RAY DIFFRACTIONr_lrange_it9.74826.8682330
X-RAY DIFFRACTIONr_lrange_other9.74726.4912292
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
1.7-1.7440.2391050.22122500.22123610.960.96299.74590.186
1.744-1.7920.2731140.21522020.21823220.9490.96799.74160.181
1.792-1.8440.2811140.19521240.19922480.9490.97299.55520.164
1.844-1.90.2341140.1920580.19221780.9640.97699.72450.159
1.9-1.9630.2041130.18220070.18321280.9710.97899.62410.151
1.963-2.0310.222890.17119570.17320590.9670.98199.36860.145
2.031-2.1080.209860.16618860.16719860.9730.98499.29510.142
2.108-2.1940.2071070.15617750.15919030.9770.98698.89650.135
2.194-2.2910.18890.14517170.14618320.9770.98798.58080.131
2.291-2.4030.159980.13816440.13917810.9850.98897.81020.124
2.403-2.5320.193800.14715480.14916690.9780.98797.54340.139
2.532-2.6850.204690.16215120.16416070.9760.98498.38210.155
2.685-2.870.212880.16813870.1714960.9710.98298.59630.165
2.87-3.0990.213650.1712990.17213850.9710.98298.48370.172
3.099-3.3930.184530.17412220.17513010.9780.98198.00150.181
3.393-3.7910.203690.16110720.16411780.9780.98496.85910.173
3.791-4.3720.145500.1549740.15410590.9880.98596.6950.175
4.372-5.3430.255420.1648240.1689000.9640.98496.22220.193
5.343-7.5050.279280.2196500.2217090.9470.97495.62760.249
7.505-45.7720.142180.1883910.1864370.9840.97893.59270.224

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