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- PDB-8vso: Ternary structure of 14-3-3 sigma, BRAF phosphopeptide (pS365) an... -

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Basic information

Entry
Database: PDB / ID: 8vso
TitleTernary structure of 14-3-3 sigma, BRAF phosphopeptide (pS365) and compound 78 (1124378)
Components
  • 14-3-3 protein sigma
  • Serine/threonine-protein kinase B-raf phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / stabilizer / protein-protein interactions
Function / homology
Function and homology information


positive regulation of axon regeneration / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / myeloid progenitor cell differentiation / SHOC2 M1731 mutant abolishes MRAS complex function ...positive regulation of axon regeneration / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / myeloid progenitor cell differentiation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / negative regulation of fibroblast migration / establishment of protein localization to membrane / positive regulation of axonogenesis / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / stress fiber assembly / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / face development / regulation of cell-cell adhesion / MAP kinase kinase activity / thyroid gland development / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / synaptic vesicle exocytosis / somatic stem cell population maintenance / positive regulation of peptidyl-serine phosphorylation / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / MAP kinase kinase kinase activity / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / postsynaptic modulation of chemical synaptic transmission / negative regulation of endothelial cell apoptotic process / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / positive regulation of protein localization / ERK1 and ERK2 cascade / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / substrate adhesion-dependent cell spreading / protein sequestering activity / cellular response to calcium ion / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / thymus development / animal organ morphogenesis / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / centriolar satellite / cellular response to xenobiotic stimulus / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / intrinsic apoptotic signaling pathway in response to DNA damage / Negative regulation of MAPK pathway / 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 / intracellular protein localization / T cell differentiation in thymus / T cell receptor signaling pathway / presynapse / MAPK cascade / regulation of cell population proliferation / regulation of protein localization / cell body / positive regulation of cell growth / scaffold protein binding / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynapse / regulation of cell cycle / neuron projection
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 B-raf / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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, BRAF phosphopeptide (pS365) and compound 78 (1124378)
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

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Assembly

Deposited unit
B: 14-3-3 protein sigma
P: Serine/threonine-protein kinase B-raf phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0646
Polymers27,5562
Non-polymers5084
Water3,909217
1
B: 14-3-3 protein sigma
P: Serine/threonine-protein kinase B-raf phosphopeptide
hetero molecules

B: 14-3-3 protein sigma
P: Serine/threonine-protein kinase B-raf phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,12712
Polymers55,1124
Non-polymers1,0168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5340 Å2
ΔGint-73 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.180, 112.457, 62.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BP

#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 B-raf phosphopeptide / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 1012.935 Da / Num. of mol.: 1 / Fragment: residues 361-369 (Uniprot numbering) / Source method: obtained synthetically / Details: containing phosphoserine 365 / Source: (synth.) Homo sapiens (human)
References: UniProt: P15056, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 221 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-WQN / 1-[8-(4-bromophenyl)sulfonyl-5-oxa-2,8-diazaspiro[3.5]nonan-2-yl]-2-chloranyl-ethanone


Mass: 423.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16BrClN2O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
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: 1.5→45.65 Å / Num. obs: 46960 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2289 / CC1/2: 0.724

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.42 Å / SU B: 1.244 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18877 2357 5 %RANDOM
Rwork0.16777 ---
obs0.16884 44581 99.95 %-
Displacement parametersBiso mean: 20.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-0 Å2
2---0.3 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 31 217 2155

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