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- PDB-6yib: 14-3-3 sigma in complex with SMAD3 pS423 peptide -

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Basic information

Entry
Database: PDB / ID: 6yib
Title14-3-3 sigma in complex with SMAD3 pS423 peptide
Components
  • 14-3-3 protein sigma
  • SMAD3
KeywordsPEPTIDE BINDING PROTEIN / Phosphorylation / PPI / signalling / SMAD
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: 1.7 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 1.2Nov 20, 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: SMAD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,10611
Polymers27,7712
Non-polymers3349
Water5,657314
1
A: 14-3-3 protein sigma
P: SMAD3
hetero molecules

A: 14-3-3 protein sigma
P: SMAD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,21122
Polymers55,5424
Non-polymers66918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6290 Å2
ΔGint-127 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.780, 111.690, 62.050
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-444-

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 SMAD3


Mass: 1228.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 323 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
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: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.7→19.74 Å / Num. obs: 31615 / % possible obs: 99.8 % / Redundancy: 12.35 % / Biso Wilson estimate: 23.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.36
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4922 / CC1/2: 0.804

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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: 1.7→19.74 Å / SU ML: 0.1458 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.858
RfactorNum. reflection% reflection
Rfree0.2033 1581 5 %
Rwork0.1666 --
obs0.1685 31595 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 14 314 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582110
X-RAY DIFFRACTIONf_angle_d0.77032870
X-RAY DIFFRACTIONf_chiral_restr0.0427312
X-RAY DIFFRACTIONf_plane_restr0.0045385
X-RAY DIFFRACTIONf_dihedral_angle_d5.3975316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.2551420.23822707X-RAY DIFFRACTION99.93
1.75-1.820.27161420.22092690X-RAY DIFFRACTION99.86
1.82-1.890.2551410.21322684X-RAY DIFFRACTION100
1.89-1.980.24321430.22012702X-RAY DIFFRACTION99.55
1.98-2.080.20671410.16812694X-RAY DIFFRACTION99.96
2.08-2.210.21471440.15792731X-RAY DIFFRACTION99.97
2.21-2.380.18381430.15912710X-RAY DIFFRACTION99.93
2.38-2.620.21621430.16082707X-RAY DIFFRACTION99.93
2.62-30.20321450.16592757X-RAY DIFFRACTION99.9
3-3.770.20261450.15412750X-RAY DIFFRACTION99.93
3.77-19.740.17941520.15682882X-RAY DIFFRACTION99.9

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