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- PDB-30tj: 14-3-3sigma protein binding to ERalpha-strong peptide (RSH mutati... -

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Basic information

Entry
Database: PDB / ID: 30tj
Title14-3-3sigma protein binding to ERalpha-strong peptide (RSH mutation) and stabilizer 3'deAc FC-A
Components
  • 14-3-3 protein sigma
  • ERa peptide pT594 strong mutant
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / peptide-protein interaction / ERalpha / 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: 2.15 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: ERa peptide pT594 strong mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8623
Polymers27,2242
Non-polymers6391
Water81145
1
A: 14-3-3 protein sigma
B: ERa peptide pT594 strong mutant
hetero molecules

A: 14-3-3 protein sigma
B: ERa peptide pT594 strong mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7256
Polymers54,4474
Non-polymers1,2782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
Buried area4100 Å2
ΔGint-15 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.95, 151.506, 75.997
Angle α, β, γ (deg.)90, 90, 90
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-426-

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 ERa peptide pT594 strong mutant


Mass: 680.648 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
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: ID30B / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.15→76 Å / Num. obs: 18393 / % possible obs: 95.5 % / Redundancy: 9.2 % / CC1/2: 0.995 / Net I/σ(I): 7.7
Reflection shellResolution: 2.15→2.21 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1548 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.123)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→75.997 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.945 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 860 4.684 %RANDOM
Rwork0.2131 17500 --
all0.215 ---
obs-18360 95.332 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.55 Å2
Baniso -1Baniso -2Baniso -3
1-3.212 Å20 Å20 Å2
2---2.476 Å20 Å2
3----0.736 Å2
Refinement stepCycle: LAST / Resolution: 2.15→75.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 45 45 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0161930
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161837
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.8292605
X-RAY DIFFRACTIONr_angle_other_deg0.4461.5714244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255.285246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.15658
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.24756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34810354
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9021089
X-RAY DIFFRACTIONr_chiral_restr0.0510.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02414
X-RAY DIFFRACTIONr_nbd_refined0.2160.2391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.21536
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2951
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.27
X-RAY DIFFRACTIONr_nbd_other0.1020.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.214
X-RAY DIFFRACTIONr_mcbond_it2.3243.28937
X-RAY DIFFRACTIONr_mcbond_other2.3243.279937
X-RAY DIFFRACTIONr_mcangle_it3.5315.891166
X-RAY DIFFRACTIONr_mcangle_other3.5335.891167
X-RAY DIFFRACTIONr_scbond_it3.3823.783993
X-RAY DIFFRACTIONr_scbond_other3.3823.782993
X-RAY DIFFRACTIONr_scangle_it5.4116.7691439
X-RAY DIFFRACTIONr_scangle_other5.4096.7671440
X-RAY DIFFRACTIONr_lrange_it6.79831.192134
X-RAY DIFFRACTIONr_lrange_other6.78931.182130
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
2.15-2.2060.35540.30913310.3113890.9040.92899.7120.3
2.206-2.2660.296540.29810480.29813750.9150.92880.14550.285
2.266-2.3320.306790.25412410.25713240.9330.95299.69790.241
2.332-2.4040.306620.24812190.25112860.9470.95599.61120.233
2.404-2.4820.392460.24812000.25312480.9010.95799.83970.232
2.482-2.5690.328530.23411640.23812200.9350.96499.75410.216
2.569-2.6660.234470.2399580.23911650.9590.96786.26610.216
2.666-2.7750.285400.22410300.22611320.950.9794.5230.196
2.775-2.8980.21500.21110300.21110850.9680.97299.53920.192
2.898-3.0390.288550.2239940.22610510.950.96699.80970.2
3.039-3.2040.275480.2229330.2249830.9520.96899.79650.207
3.204-3.3980.289420.2139140.2169560.9480.9721000.2
3.398-3.6320.202290.1957130.1958760.9720.97984.70320.183
3.632-3.9220.205350.1955730.1968470.9750.97971.78280.181
3.922-4.2950.236380.1747380.1777760.9770.9841000.17
4.295-4.80.22330.1626630.1656960.9730.9841000.163
4.8-5.5390.202410.2055700.2056110.9750.9781000.205
5.539-6.7750.288270.2175160.2215440.9650.97599.81620.218
6.775-9.5430.253120.1764130.1784270.9750.98299.53160.184
9.543-75.9970.246150.2732520.2712680.9380.93799.62690.289
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79060.0165-0.1091.32210.69622.06-0.0307-0.03530.04460.1478-0.08690.20270.0772-0.22130.11770.0288-0.0080.01850.0334-0.01070.06-8.516-20.454-21.107
214.1686-3.28573.141414.94781.93759.00790.1531.04550.2913-0.8283-0.2780.162-0.52580.24620.1250.1093-0.01350.00690.09470.01530.0341-11.689-11.909-25.481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA-4 - 231
2X-RAY DIFFRACTION2ALLB591 - 595

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