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- PDB-9qni: NOTCH4 phosphopeptide binding to 14-3-3sigma -

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Basic information

Entry
Database: PDB / ID: 9qni
TitleNOTCH4 phosphopeptide binding to 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • NOTCH4 pS1847 peptide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 protein-protein interactions
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 protein kinase activity / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / 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 / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / 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 / cytoplasm / cytosol
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: 1.8 Å
AuthorsPennings, M.A.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101077879European Union
CitationJournal: Digit Discov / Year: 2025
Title: Identifying 14-3-3 interactome binding sites with deep learning.
Authors: van Weesep, L. / Ozcelik, R. / Pennings, M. / Criscuolo, E. / Ottmann, C. / Brunsveld, L. / Grisoni, F.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: NOTCH4 pS1847 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5387
Polymers27,3432
Non-polymers1965
Water2,198122
1
A: 14-3-3 protein sigma
P: NOTCH4 pS1847 peptide
hetero molecules

A: 14-3-3 protein sigma
P: NOTCH4 pS1847 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,07714
Polymers54,6854
Non-polymers39210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4630 Å2
ΔGint-94 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.064, 113.004, 63.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

CA

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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 NOTCH4 pS1847 peptide


Mass: 799.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.71 Å3/Da / Density % sol: 54.7 %
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: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.8→66.93 Å / Num. obs: 23185 / % possible obs: 82.8 % / Redundancy: 9 % / CC1/2: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1612 / CC1/2: 0.805

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→66.93 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.467 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20748 1173 5.1 %RANDOM
Rwork0.16935 ---
obs0.17129 21991 82.83 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.859 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å2-0 Å2
2---0.52 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→66.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 5 122 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0161940
X-RAY DIFFRACTIONr_bond_other_d00.0161843
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.8222612
X-RAY DIFFRACTIONr_angle_other_deg0.4551.5674261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0615.272257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09610366
X-RAY DIFFRACTIONr_chiral_restr0.0540.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
X-RAY DIFFRACTIONr_mcbond_it12.2412.889972
X-RAY DIFFRACTIONr_mcbond_other12.2182.889972
X-RAY DIFFRACTIONr_mcangle_it10.485.1041212
X-RAY DIFFRACTIONr_mcangle_other10.495.111213
X-RAY DIFFRACTIONr_scbond_it22.9893.78968
X-RAY DIFFRACTIONr_scbond_other22.9873.777968
X-RAY DIFFRACTIONr_scangle_other17.8236.2591400
X-RAY DIFFRACTIONr_long_range_B_refined17.98132.072216
X-RAY DIFFRACTIONr_long_range_B_other18.06631.142191
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 110 -
Rwork0.224 1924 -
obs--99.95 %

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