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- PDB-8b2k: Ternary structure of 14-3-3s, RND3 phosphopeptide and dual-reacti... -

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Basic information

Entry
Database: PDB / ID: 8b2k
TitleTernary structure of 14-3-3s, RND3 phosphopeptide and dual-reactive compound 10
Components
  • 14-3-3 protein sigma
  • Rho-related GTP-binding protein RhoE
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / dual-reactive compound
Function / homology
Function and homology information


RND3 GTPase cycle / small GTPase-mediated signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation ...RND3 GTPase cycle / small GTPase-mediated signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / 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 / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / stem cell proliferation / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / cell migration / regulation of protein localization / actin cytoskeleton organization / positive regulation of cell growth / regulation of cell cycle / cell adhesion / cadherin binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho-related GTP-binding protein RhoE / Small GTPase Rho / small GTPase Rho family profile. / 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 ...Rho-related GTP-binding protein RhoE / Small GTPase Rho / small GTPase Rho family profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-OQ3 / 14-3-3 protein sigma / Rho-related GTP-binding protein RhoE
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERR gamma Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach.
Authors: Somsen, B.A. / Schellekens, R.J.C. / Verhoef, C.J.A. / Arkin, M.R. / Ottmann, C. / Cossar, P.J. / Brunsveld, L.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6447
Polymers28,2342
Non-polymers4115
Water5,837324
1
A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules

A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,28914
Polymers56,4684
Non-polymers82110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area3710 Å2
ΔGint-74 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.431, 112.183, 62.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 26553.875 Da / Num. of mol.: 1 / Mutation: C38N
Source method: isolated from a genetically manipulated source
Details: GAMGS at the beginning (-5 to -1) are part of the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Rho-related GTP-binding protein RhoE / Protein MemB / Rho family GTPase 3 / Rho-related GTP-binding protein Rho8 / Rnd3


Mass: 1679.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61587

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Non-polymers , 4 types, 329 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-OQ3 / 3-bromanyl-5-methanoyl-~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide


Mass: 302.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12BrNO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 26% PEG400, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→45.56 Å / Num. obs: 57171 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 41.5
Reflection shellResolution: 1.4→1.43 Å / Mean I/σ(I) obs: 17.6 / Num. unique obs: 34011 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
Cootmodel building
REFMAC5.8.0267refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y1d

6y1d


Resolution: 1.4→45.56 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 5472 4.97 %
Rwork0.1666 104557 -
obs0.1672 57148 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.39 Å2 / Biso mean: 15.3934 Å2 / Biso min: 2.41 Å2
Refinement stepCycle: final / Resolution: 1.4→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 20 324 2224
Biso mean--18.84 25.97 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.24761670.19683475364298
1.42-1.430.20321520.184134713623100
1.43-1.450.1791620.171635353697100
1.45-1.470.19312100.164534023612100
1.47-1.490.19232140.163534813695100
1.49-1.510.19351990.159935343733100
1.51-1.530.19281870.166334293616100
1.53-1.550.17831320.166435053637100
1.55-1.580.16511910.16735213712100
1.58-1.60.19292050.161834623667100
1.6-1.630.20511720.165234583630100
1.63-1.660.19261650.154935363701100
1.66-1.690.19791870.156334873674100
1.69-1.730.16721710.165235053676100
1.73-1.770.19112210.164934383659100
1.77-1.810.24171670.170934963663100
1.81-1.850.20751580.166634883646100
1.85-1.90.1612250.172534803705100
1.9-1.960.1831800.168734823662100
1.96-2.020.18261870.163134713658100
2.02-2.090.17531620.152635183680100
2.09-2.180.1621840.154235403724100
2.18-2.280.15861810.152334443625100
2.28-2.40.16841780.155535033681100
2.4-2.550.17051620.167734953657100
2.55-2.740.19182170.175634663683100
2.74-3.020.14621750.181334893664100
3.02-3.460.19352100.168534613671100
3.46-4.350.16852100.156934653675100
4.35-45.560.17151410.186135203661100

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