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- PDB-8vsn: Ternary structure of 14-3-3 sigma, ARAF phosphopeptide (pS214) an... -

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Basic information

Entry
Database: PDB / ID: 8vsn
TitleTernary structure of 14-3-3 sigma, ARAF phosphopeptide (pS214) and compound 79 (1124379)
Components
  • 14-3-3 protein sigma
  • Serine/threonine-protein kinase A-Raf phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / stabilizer / protein-protein interactions
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of TOR signaling / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / 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 proteasomal ubiquitin-dependent protein catabolic process / regulation of TOR signaling / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / 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 / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / 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 / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / protein modification process / Negative regulation of MAPK pathway / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / MAPK cascade / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / non-specific serine/threonine protein kinase / protein kinase activity / regulation of cell cycle / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / 14-3-3 protein sigma / Zinc finger phorbol-ester/DAG-type profile. ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / 14-3-3 protein sigma / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein kinase A-Raf / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsVickery, H.R. / Virta, J.M. / Pennings, M. / Konstantinidou, M. / van den Oetelaar, M. / Neitz, R.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: Ternary structure of 14-3-3 sigma, ARAF phosphopeptide (pS214) and compound 79 (1124379)
Authors: Vickery, H.R. / Virta, J.M. / Pennings, M. / Konstantinidou, M. / van den Oetelaar, M. / Neitz, R.J. / Ottmann, C. / Brunsveld, L. / Arkin, M.R.
History
DepositionJan 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 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
P: Serine/threonine-protein kinase A-Raf phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6047
Polymers28,0252
Non-polymers5795
Water2,792155
1
A: 14-3-3 protein sigma
P: Serine/threonine-protein kinase A-Raf phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
P: Serine/threonine-protein kinase A-Raf phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,20714
Polymers56,0494
Non-polymers1,15810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area6220 Å2
ΔGint-83 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.576, 150.225, 76.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 26542.914 Da / Num. of mol.: 1 / Fragment: residues 1-231
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 Serine/threonine-protein kinase A-Raf phosphopeptide / Proto-oncogene A-Raf / Proto-oncogene A-Raf-1 / Proto-oncogene Pks


Mass: 1481.594 Da / Num. of mol.: 1 / Fragment: residues 209-220 (Uniprot numbering) / Source method: obtained synthetically / Details: containing phosphoserine 214 / Source: (synth.) Homo sapiens (human)
References: UniProt: P10398, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 160 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: 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.: 1 / Source method: obtained synthetically / Formula: C14H16ClIN2O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG4000, HEPES, CaCl2, glycerol

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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: 1.91→57.76 Å / Num. obs: 58185 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 19.8
Reflection shellResolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1897 / CC1/2: 0.631

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Processing

Software
NameVersionClassification
PDB-REDO5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→57.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.426 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27206 2950 5.1 %RANDOM
Rwork0.23981 ---
obs0.24141 55234 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.795 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å2-0 Å20 Å2
2---0.46 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.91→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 26 155 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131948
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151835
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6492628
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5854234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85522.404104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76515353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3711514
X-RAY DIFFRACTIONr_chiral_restr0.080.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7084.148967
X-RAY DIFFRACTIONr_mcbond_other3.6974.145966
X-RAY DIFFRACTIONr_mcangle_it5.0266.2011204
X-RAY DIFFRACTIONr_mcangle_other5.0256.2061205
X-RAY DIFFRACTIONr_scbond_it5.0234.521981
X-RAY DIFFRACTIONr_scbond_other5.0254.522982
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0036.6311422
X-RAY DIFFRACTIONr_long_range_B_refined8.94378.5358415
X-RAY DIFFRACTIONr_long_range_B_other8.89278.4688291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→57.76 Å
RfactorNum. reflection% reflection
Rfree0.614 218 -
Rwork0.616 3988 -
obs--99.01 %

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