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- PDB-8bwh: Small molecule stabilizer for 14-3-3/ChREBP (Cmd 42) -

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Basic information

Entry
Database: PDB / ID: 8bwh
TitleSmall molecule stabilizer for 14-3-3/ChREBP (Cmd 42)
Components
  • 14-3-3 protein sigma
  • Carbohydrate-responsive element-binding protein
KeywordsSTRUCTURAL PROTEIN / 14-3-3 / ChREBP / stabilization
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / 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
: / MLX interacting protein like / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPennings, M.A.M. / Visser, E.J. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Biorxiv / Year: 2024
Title: Molecular glues of the regulatory ChREBP/14-3-3 complex protect beta cells from glucolipotoxicity.
Authors: Katz, L.S. / Visser, E.J. / Plitzko, K.F. / Pennings, M. / Cossar, P.J. / Tse, I.L. / Kaiser, M. / Brunsveld, L. / Scott, D.K. / Ottmann, C.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: 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
B: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3896
Polymers28,9272
Non-polymers4624
Water2,450136
1
A: 14-3-3 protein sigma
B: Carbohydrate-responsive element-binding protein
hetero molecules

A: 14-3-3 protein sigma
B: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,77812
Polymers57,8534
Non-polymers9248
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)63.166, 147.336, 77.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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 Carbohydrate-responsive element-binding protein /


Mass: 2383.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JDF5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-XSL / [2-[2-[[2,2-bis(fluoranyl)-2-(2-fluorophenyl)ethyl]amino]-2-oxidanylidene-ethoxy]phenyl]phosphonic acid


Mass: 389.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15F3NO5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES (pH 7.1), PEG400 (24% (v/v)), 0.19 M CaCl2 and 5% (v/v) Glycerol

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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 PILATUS3 2M / Detector: PIXEL / Date: Jan 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.1→34.66 Å / Num. obs: 20542 / % possible obs: 97.2 % / Redundancy: 4.4 % / CC1/2: 0.987 / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1700 / CC1/2: 0.671

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Processing

Software
NameVersionClassification
REFMAC8refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 2.1→34.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.992 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26388 1058 5.2 %RANDOM
Rwork0.21636 ---
obs0.21884 19310 95.1 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2--0.46 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 29 136 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0162085
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161902
X-RAY DIFFRACTIONr_angle_refined_deg0.7831.8212808
X-RAY DIFFRACTIONr_angle_other_deg0.3171.5634438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1215.299268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.73101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79310388
X-RAY DIFFRACTIONr_chiral_restr0.0340.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
X-RAY DIFFRACTIONr_mcbond_it10.0793.5981014
X-RAY DIFFRACTIONr_mcbond_other10.0773.5981014
X-RAY DIFFRACTIONr_mcangle_it11.645.3571264
X-RAY DIFFRACTIONr_mcangle_other11.6365.361265
X-RAY DIFFRACTIONr_scbond_it12.5354.0561071
X-RAY DIFFRACTIONr_scbond_other12.5364.0561071
X-RAY DIFFRACTIONr_scangle_other14.8525.8151545
X-RAY DIFFRACTIONr_long_range_B_refined16.26645.1452460
X-RAY DIFFRACTIONr_long_range_B_other16.34844.9642427
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 77 -
Rwork0.281 1431 -
obs--98.63 %

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