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- PDB-6yic: 14-3-3 sigma in complex with SMAD4 pS403 peptide -

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Basic information

Entry
Database: PDB / ID: 6yic
Title14-3-3 sigma in complex with SMAD4 pS403 peptide
Components
  • 14-3-3 protein sigma
  • SMAD4
KeywordsPEPTIDE BINDING PROTEIN / phosphorylation / SMAD / signalling / PPI
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 / 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 / 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 domain / Delta-Endotoxin; domain 1 / 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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKiehstaller, S. / Graf, S. / Hennig, S.
CitationJournal: To Be Published
Title: Identification and characterization of 14-3-3/SMAD protein-protein-interactions
Authors: Graf, S. / Kiehstaller, S. / Ottmann, C. / Hennig, S.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: SMAD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9648
Polymers27,7372
Non-polymers2276
Water5,837324
1
A: 14-3-3 protein sigma
P: SMAD4
hetero molecules

A: 14-3-3 protein sigma
P: SMAD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92816
Polymers55,4744
Non-polymers45412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5380 Å2
ΔGint-111 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.990, 111.830, 62.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-718-

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
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 SMAD4


Mass: 1194.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 330 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1 M HEPES pH7.5 0.19 M CaCl2 5% glycerol 28% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.6→45.36 Å / Num. obs: 38169 / % possible obs: 100 % / Redundancy: 13.21 % / Biso Wilson estimate: 24.99 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.86
Reflection shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 1.91 / Num. unique obs: 6243 / CC1/2: 0.748

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC7.0.024refinement
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.6→45.36 Å / SU ML: 0.1829 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2889
RfactorNum. reflection% reflection
Rfree0.2049 1909 5.01 %
Rwork0.1676 --
obs0.1694 38141 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 11 324 2182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542040
X-RAY DIFFRACTIONf_angle_d0.74782787
X-RAY DIFFRACTIONf_chiral_restr0.0434312
X-RAY DIFFRACTIONf_plane_restr0.0038362
X-RAY DIFFRACTIONf_dihedral_angle_d5.2804314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28551350.26182554X-RAY DIFFRACTION99.93
1.64-1.680.2661330.23662522X-RAY DIFFRACTION99.81
1.68-1.730.25431360.2392590X-RAY DIFFRACTION99.96
1.73-1.790.2641340.23042539X-RAY DIFFRACTION100
1.79-1.850.27631340.21142557X-RAY DIFFRACTION100
1.85-1.930.21021350.18852567X-RAY DIFFRACTION99.96
1.93-2.020.23181360.17562569X-RAY DIFFRACTION99.96
2.02-2.120.20351350.16552573X-RAY DIFFRACTION100
2.12-2.260.21761360.15762574X-RAY DIFFRACTION100
2.26-2.430.19691360.15882591X-RAY DIFFRACTION100
2.43-2.670.1831370.16492601X-RAY DIFFRACTION100
2.67-3.060.21641370.16272604X-RAY DIFFRACTION100
3.06-3.860.17731400.15072653X-RAY DIFFRACTION100
3.86-45.360.19911450.16032738X-RAY DIFFRACTION99.97

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