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- PDB-7b13: 14-3-3sigma in complex with SHN3pS542 phosphopeptide crystal structure -

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Basic information

Entry
Database: PDB / ID: 7b13
Title14-3-3sigma in complex with SHN3pS542 phosphopeptide crystal structure
Components
  • 14-3-3 protein sigma
  • SHN3pS542
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: 1.37 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 13, 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: SHN3pS542
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6826
Polymers27,5852
Non-polymers974
Water7,404411
1
A: 14-3-3 protein sigma
P: SHN3pS542
hetero molecules

A: 14-3-3 protein sigma
P: SHN3pS542
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36412
Polymers55,1704
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5810 Å2
ΔGint-93 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.760, 112.830, 62.930
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-301-

MG

21A-791-

HOH

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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 SHN3pS542


Mass: 1042.061 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.: 411 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
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: 1.37→28.46 Å / Num. obs: 61661 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.51 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.1
Reflection shellResolution: 1.37→1.4 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 3003 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
XDS1.16_3549data reduction
Aimless1.16_3549data scaling
PHASERphasing
PHENIX1.71.1-3600refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.37→28.21 Å / SU ML: 0.1173 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1697 3031 4.92 %
Rwork0.1497 58580 -
obs0.1507 61611 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.66 Å2
Refinement stepCycle: LAST / Resolution: 1.37→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 4 411 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182192
X-RAY DIFFRACTIONf_angle_d1.5643006
X-RAY DIFFRACTIONf_chiral_restr0.0864334
X-RAY DIFFRACTIONf_plane_restr0.0096394
X-RAY DIFFRACTIONf_dihedral_angle_d18.7804914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.28271470.23082621X-RAY DIFFRACTION99.68
1.39-1.420.22471200.21092612X-RAY DIFFRACTION99.71
1.42-1.440.23851380.20112633X-RAY DIFFRACTION99.57
1.44-1.470.22971280.18512649X-RAY DIFFRACTION99.75
1.47-1.50.1871570.17842607X-RAY DIFFRACTION99.89
1.5-1.530.21151380.16712626X-RAY DIFFRACTION99.96
1.53-1.560.20771520.16692625X-RAY DIFFRACTION99.89
1.56-1.60.16671520.1572654X-RAY DIFFRACTION99.93
1.6-1.640.17391290.14872635X-RAY DIFFRACTION99.93
1.64-1.680.17361270.15082649X-RAY DIFFRACTION99.82
1.68-1.730.18191600.14892626X-RAY DIFFRACTION99.96
1.73-1.790.18311200.14852667X-RAY DIFFRACTION99.96
1.79-1.850.15551350.14722671X-RAY DIFFRACTION100
1.85-1.920.16941250.1522672X-RAY DIFFRACTION99.93
1.92-2.010.16121360.14762645X-RAY DIFFRACTION99.89
2.01-2.120.16081210.13922681X-RAY DIFFRACTION99.96
2.12-2.250.15821350.13512682X-RAY DIFFRACTION100
2.25-2.420.14661480.12772674X-RAY DIFFRACTION100
2.42-2.670.15451370.13522671X-RAY DIFFRACTION100
2.67-3.050.16861400.14342719X-RAY DIFFRACTION100
3.05-3.840.14381400.13592720X-RAY DIFFRACTION99.97
3.84-28.210.18021460.16372841X-RAY DIFFRACTION99.9

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