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- PDB-7b15: 14-3-3sigma in complex with SHN3pT869 phosphopeptide crystal structure -

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Basic information

Entry
Database: PDB / ID: 7b15
Title14-3-3sigma in complex with SHN3pT869 phosphopeptide crystal structure
Components
  • 14-3-3 protein sigma
  • SHN3pT869
KeywordsPEPTIDE BINDING PROTEIN / Adaptor Protein / Phosphorylation
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSoini, L. / Leysen, S. / Davis, J. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission675179 Netherlands
CitationJournal: To Be Published
Title: 14-3-3 sigma in complex with phosphopeptides
Authors: Soini, L. / Leysen, S. / Davis, J. / Ottmann, C.
History
DepositionNov 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
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: SHN3pT869
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7766
Polymers27,6792
Non-polymers974
Water7,098394
1
A: 14-3-3 protein sigma
P: SHN3pT869
hetero molecules

A: 14-3-3 protein sigma
P: SHN3pT869
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,55212
Polymers55,3584
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5290 Å2
ΔGint-67 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.299, 113.450, 63.200
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-302-

MG

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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 SHN3pT869


Mass: 1136.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7.5
Details: 95 mM Hepes pH 7.1-7.7, 24-29% PEG400, 190 mM Cacl2, Glycerol 5%
PH range: 7.1-7.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.59→56.72 Å / Num. obs: 40935 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.39 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3
Reflection shellResolution: 1.59→1.61 Å / Rmerge(I) obs: 0.15 / Num. unique obs: 1998 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1-3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.59→29.65 Å / SU ML: 0.0997 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.42
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1586 2042 4.99 %
Rwork0.1398 38862 -
obs0.1407 40904 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.16 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 4 394 2332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092188
X-RAY DIFFRACTIONf_angle_d1.02183001
X-RAY DIFFRACTIONf_chiral_restr0.0486332
X-RAY DIFFRACTIONf_plane_restr0.0066396
X-RAY DIFFRACTIONf_dihedral_angle_d14.55681447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.620.17231260.15122572X-RAY DIFFRACTION99.59
1.62-1.660.16551380.14332561X-RAY DIFFRACTION99.59
1.66-1.710.14881210.14262545X-RAY DIFFRACTION99.37
1.71-1.760.1611460.14112549X-RAY DIFFRACTION99.01
1.76-1.810.19871330.14552554X-RAY DIFFRACTION99.96
1.81-1.880.18481290.14552550X-RAY DIFFRACTION99.96
1.88-1.950.18011310.14542599X-RAY DIFFRACTION99.96
1.95-2.040.18251520.13852549X-RAY DIFFRACTION99.93
2.04-2.150.14471580.12862562X-RAY DIFFRACTION100
2.15-2.290.1411270.12422585X-RAY DIFFRACTION100
2.29-2.460.15471380.12342600X-RAY DIFFRACTION100
2.46-2.710.16621280.13092631X-RAY DIFFRACTION100
2.71-3.10.15651430.13912600X-RAY DIFFRACTION99.96
3.1-3.910.14121490.1322642X-RAY DIFFRACTION100
3.91-29.650.16271230.16152763X-RAY DIFFRACTION99.76

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