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- PDB-8qsd: Ternary structure of 14-3-3s, BRAF phosphopeptide (pS365) and com... -

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Basic information

Entry
Database: PDB / ID: 8qsd
TitleTernary structure of 14-3-3s, BRAF phosphopeptide (pS365) and compound 79 (1124379).
Components
  • 14-3-3 protein sigma
  • BRAF peptide pS365
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / protein-protein interaction stabilizer
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 / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / 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: 2 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
H: BRAF peptide pS365
J: 14-3-3 protein sigma
S: BRAF peptide pS365
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,54614
Polymers55,3884
Non-polymers1,15810
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-68 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.277, 63.621, 73.294
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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

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


Mass: 26542.914 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 BRAF peptide pS365


Mass: 1151.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 366 molecules

#3: Chemical ChemComp-WQT / 2-chloranyl-1-[8-(4-iodophenyl)sulfonyl-5-oxa-2,8-diazaspiro[3.5]nonan-2-yl]ethanone


Mass: 470.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16ClIN2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
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: Jul 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 2→58.31 Å / Num. obs: 44841 / % possible obs: 98.5 % / Redundancy: 6.5 % / CC1/2: 0.994 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3328 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→58.31 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2214 4.95 %RANDOM
Rwork0.216 ---
obs0.217 44772 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→58.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 52 356 4161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008505
X-RAY DIFFRACTIONf_angle_d0.884485
X-RAY DIFFRACTIONf_dihedral_angle_d10.399557
X-RAY DIFFRACTIONf_chiral_restr0.049573
X-RAY DIFFRACTIONf_plane_restr0.008672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.33461290.2832672X-RAY DIFFRACTION99
2.04-2.090.3271330.26412658X-RAY DIFFRACTION99
2.09-2.140.28121410.23842655X-RAY DIFFRACTION99
2.14-2.20.29771400.2292677X-RAY DIFFRACTION99
2.2-2.270.27521290.22422619X-RAY DIFFRACTION97
2.27-2.340.2561280.22722418X-RAY DIFFRACTION91
2.34-2.420.26691300.22762481X-RAY DIFFRACTION91
2.42-2.520.23461280.22182685X-RAY DIFFRACTION99
2.52-2.630.27041470.22122680X-RAY DIFFRACTION100
2.63-2.770.23381400.21772712X-RAY DIFFRACTION100
2.77-2.950.21491280.2352700X-RAY DIFFRACTION100
2.95-3.170.251350.22712702X-RAY DIFFRACTION100
3.17-3.490.26121380.21512720X-RAY DIFFRACTION100
3.49-40.22811450.19262715X-RAY DIFFRACTION100
4-5.040.17761640.19332698X-RAY DIFFRACTION100
5.04-58.310.22311590.21392766X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -20.6723 Å / Origin y: -31.7738 Å / Origin z: 4.6265 Å
111213212223313233
T0.2177 Å20.0491 Å2-0.0143 Å2-0.2124 Å20.0179 Å2--0.262 Å2
L0.606 °2-0.0112 °2-0.0361 °2-0.5271 °20.0465 °2--1.7656 °2
S0.0497 Å °0.0427 Å °0.0202 Å °-0.058 Å °-0.1021 Å °-0.0796 Å °0.1905 Å °0.0767 Å °-0.0238 Å °
Refinement TLS groupSelection details: all

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