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- PDB-8qs3: Ternary structure of 14-3-3s, C-RAF phosphopeptide (pS259) and co... -

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Basic information

Entry
Database: PDB / ID: 8qs3
TitleTernary structure of 14-3-3s, C-RAF phosphopeptide (pS259) and compound 23 (1083848)
Components
  • 14-3-3 protein sigma
  • C-RAF peptide pS259
KeywordsPEPTIDE BINDING PROTEIN / Stabilizer / protein-protein interaction
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 cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / 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 / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of protein kinase activity / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / 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
: / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKonstantinidou, M. / Vickery, H. / Pennings, M.A.M. / Virta, J. / Visser, E.J. / Oetelaar, M.C.M. / Overmans, M. / Neitz, J. / Ottmann, C. / Brunsveld, L. / Arkin, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147696 United States
CitationJournal: To Be Published
Title: Small molecule stabilization of the 14-3-3sigma/CRAF complex inhibits the MAPK pathway
Authors: Konstantinidou, M. / Vickery, H. / Pennings, M.A.M. / Virta, J. / Visser, E.J. / Oetelaar, M.C.M. / Overmans, M. / Neitz, J. / Ottmann, C. / Brunsveld, L. / Arkin, M.R.
History
DepositionOct 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: 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
K: C-RAF peptide pS259
M: 14-3-3 protein sigma
Y: C-RAF peptide pS259
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,68620
Polymers55,3884
Non-polymers1,29816
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-110 kcal/mol
Surface area22350 Å2
Unit cell
Length a, b, c (Å)60.685, 89.262, 116.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules AMKY

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


Mass: 26485.865 Da / Num. of mol.: 2
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 C-RAF peptide pS259


Mass: 1208.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 462 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-WQI / 2-chloranyl-~{N}-[[1-(4-iodophenyl)sulfonylpiperidin-4-yl]methyl]ethanamide


Mass: 456.727 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18ClIN2O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 57.02 %
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: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.6→116.97 Å / Num. obs: 83028 / % possible obs: 98.2 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4109 / CC1/2: 0.727

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→70.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.017 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19922 4186 5 %RANDOM
Rwork0.18397 ---
obs0.18475 78774 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.84 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 56 446 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0163909
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163695
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.8235266
X-RAY DIFFRACTIONr_angle_other_deg0.4511.5688541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2025.277505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.45552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29210727
X-RAY DIFFRACTIONr_chiral_restr0.0520.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
X-RAY DIFFRACTIONr_mcbond_it1.9141.9051923
X-RAY DIFFRACTIONr_mcbond_other1.9141.9051923
X-RAY DIFFRACTIONr_mcangle_it2.8273.4112395
X-RAY DIFFRACTIONr_mcangle_other2.8273.4112396
X-RAY DIFFRACTIONr_scbond_it3.3082.2961986
X-RAY DIFFRACTIONr_scbond_other3.3092.2951984
X-RAY DIFFRACTIONr_scangle_other5.0994.0392872
X-RAY DIFFRACTIONr_long_range_B_refined7.48921.074755
X-RAY DIFFRACTIONr_long_range_B_other7.39519.934622
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 306 -
Rwork0.275 5864 -
obs--100 %
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)
10.5064-0.32560.05141.8162-0.60460.64830.0389-0.0019-0.1282-0.1186-0.02020.12190.0046-0.0296-0.01870.01130.0074-0.00820.0930.00850.098-26.119-21.4188.438
25.90170.8378-1.191112.4801-2.748310.06560.1239-0.3317-0.25290.4492-0.128-0.4709-0.27180.38710.00410.08780.0422-0.07490.1097-0.00710.1007-19.794-15.40812.486
32.50170.0019-0.89510.6953-0.07941.32550.0361-0.40880.11350.12910.0314-0.0509-0.02710.2158-0.06750.02510.00260.00020.1311-0.00580.11250.075-39.33329.016
45.2367-1.30011.47996.8139-1.112212.470.1824-0.35120.6670.0433-0.04190.2046-0.6067-0.1195-0.14050.05420.00710.0380.1307-0.09790.3088-0.884-30.95231.757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2K255 - 264
2X-RAY DIFFRACTION4Y255 - 264

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