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- PDB-9qnh: Myc pS294 phosphopeptide binding to 14-3-3sigma -

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Basic information

Entry
Database: PDB / ID: 9qnh
TitleMyc pS294 phosphopeptide binding to 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • Myc proto-oncogene protein
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 protein-protein interactions
Function / homology
Function and homology information


positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters ...positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / myotube differentiation / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / response to alkaloid / B cell apoptotic process / transcription regulator activator activity / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / regulation of telomere maintenance / middle ear morphogenesis / skeletal system morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / regulation of epidermal cell division / protein kinase C inhibitor activity / rRNA metabolic process / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / positive regulation of telomere maintenance / regulation of cell-cell adhesion / E-box binding / skeletal muscle cell differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / positive regulation of transcription initiation by RNA polymerase II / establishment of skin barrier / chromosome organization / 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 fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / ERK1 and ERK2 cascade / 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 / positive regulation of epithelial cell proliferation / stem cell proliferation / transcription coregulator binding / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / euchromatin / MAPK6/MAPK4 signaling / protein processing / NOTCH1 Intracellular Domain Regulates Transcription / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / spindle / Wnt signaling pathway / cellular response to xenobiotic stimulus / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / intracellular protein localization / MAPK cascade
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / 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 / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
Myc proto-oncogene protein / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Myc proto-oncogene protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,87510
Polymers27,5592
Non-polymers3168
Water5,044280
1
A: 14-3-3 protein sigma
P: Myc proto-oncogene protein
hetero molecules

A: 14-3-3 protein sigma
P: Myc proto-oncogene protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,75020
Polymers55,1184
Non-polymers63216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5690 Å2
ΔGint-139 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.851, 112.721, 62.964
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-306-

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 Myc proto-oncogene protein / Class E basic helix-loop-helix protein 39 / bHLHe39 / Proto-oncogene c-Myc / Transcription factor p64


Mass: 1015.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01106
#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.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
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: 1.3→66.76 Å / Num. obs: 63609 / % possible obs: 88.3 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 31.2
Reflection shellResolution: 1.3→1.33 Å / Mean I/σ(I) obs: 5.4 / Num. unique obs: 3459 / CC1/2: 0.948

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.85 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.421 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1674 3237 5.1 %RANDOM
Rwork0.13872 ---
obs0.14022 60348 88.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.939 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å2-0 Å2
2---0.91 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 8 280 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0162031
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161954
X-RAY DIFFRACTIONr_angle_refined_deg0.9111.8272749
X-RAY DIFFRACTIONr_angle_other_deg0.411.5684525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875.282284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59210397
X-RAY DIFFRACTIONr_chiral_restr0.0430.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_mcbond_it55.7261.4061004
X-RAY DIFFRACTIONr_mcbond_other55.7211.4071004
X-RAY DIFFRACTIONr_mcangle_it75.4352.471258
X-RAY DIFFRACTIONr_mcangle_other75.4082.4741259
X-RAY DIFFRACTIONr_scbond_it93.0242.1321027
X-RAY DIFFRACTIONr_scbond_other93.0132.131027
X-RAY DIFFRACTIONr_scangle_other3.4651479
X-RAY DIFFRACTIONr_long_range_B_refined22.472461
X-RAY DIFFRACTIONr_long_range_B_other20.062375
X-RAY DIFFRACTIONr_rigid_bond_restr9.04233985
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 282 -
Rwork0.171 4924 -
obs--98.65 %
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)
10.62290.2662-0.34550.5303-0.21690.7563-0.03240.03830.0014-0.03630.0213-0.01750.03970.03620.01120.0035-0.00040.00120.00860.00080.0009-23.97616.799-8.039
214.04710.0263-5.92619.34410.01469.4253-0.2803-0.4175-0.61070.14870.165-0.5130.86941.06480.11540.10930.0788-0.03460.17280.03520.1253-14.94512.52-9.767

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