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- PDB-6ylu: 14-3-3sigma in complex with BLNKpT152 phosphopeptide crystal structure -

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Basic information

Entry
Database: PDB / ID: 6ylu
Title14-3-3sigma in complex with BLNKpT152 phosphopeptide crystal structure
Components
  • 14-3-3 protein sigma
  • BLNKpT152
KeywordsPEPTIDE BINDING PROTEIN / Adaptor Protein / Phosphorylation
Function / homology
Function and homology information


transmembrane receptor protein tyrosine kinase adaptor activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / phospholipase binding / Regulation of localization of FOXO transcription factors / humoral immune response ...transmembrane receptor protein tyrosine kinase adaptor activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / phospholipase binding / Regulation of localization of FOXO transcription factors / humoral immune response / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / positive regulation of protein localization / RHO GTPases activate PKNs / cell surface receptor protein tyrosine kinase signaling pathway / protein kinase A signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / SH2 domain binding / B cell differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / protein tyrosine kinase binding / positive regulation of protein export from nucleus / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Regulation of signaling by CBL / B cell receptor signaling pathway / negative regulation of protein kinase activity / molecular condensate scaffold activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / Potential therapeutics for SARS / regulation of cell cycle / intracellular signal transduction / cadherin binding / inflammatory response / intracellular membrane-bounded organelle / lipid binding / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
14-3-3 protein sigma / B-cell linker protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSoini, L. / Leysen, S. / Davis, J. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission675179 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2020
Title: 14-3-3sigma in complex with BLNKpT152 phosphopeptide crystal structure
Authors: Soini, L. / Leysen, S. / Davis, J. / Ottmann, C.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: 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 23, 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
B: BLNKpT152
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9115
Polymers27,8382
Non-polymers733
Water6,972387
1
A: 14-3-3 protein sigma
B: BLNKpT152
hetero molecules

A: 14-3-3 protein sigma
B: BLNKpT152
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,82210
Polymers55,6774
Non-polymers1466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5070 Å2
ΔGint-57 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.250, 112.110, 62.520
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-413-

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 BLNKpT152


Mass: 1295.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WV28*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / 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: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.88→26.63 Å / Num. obs: 23758 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.73 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.089 / Rrim(I) all: 0.152 / Net I/σ(I): 8.8
Reflection shellResolution: 1.88→1.93 Å / Num. unique obs: 1473 / CC1/2: 0.915

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Processing

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

3mhr


Resolution: 1.88→26.63 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.393
RfactorNum. reflection% reflection
Rfree0.2111 1157 4.88 %
Rwork0.1577 --
obs0.1603 23726 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.57 Å2
Refinement stepCycle: LAST / Resolution: 1.88→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 3 387 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612112
X-RAY DIFFRACTIONf_angle_d0.80462881
X-RAY DIFFRACTIONf_chiral_restr0.0424321
X-RAY DIFFRACTIONf_plane_restr0.0043376
X-RAY DIFFRACTIONf_dihedral_angle_d12.514321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.970.28021350.18862754X-RAY DIFFRACTION100
1.97-2.070.23881280.16372829X-RAY DIFFRACTION100
2.07-2.20.19821400.15062780X-RAY DIFFRACTION100
2.2-2.370.20451640.14652768X-RAY DIFFRACTION100
2.37-2.610.21631480.16312813X-RAY DIFFRACTION99.93
2.61-2.990.231550.17612815X-RAY DIFFRACTION99.76
2.99-3.760.19491430.14132856X-RAY DIFFRACTION99.93
3.76-26.630.18891440.15652954X-RAY DIFFRACTION99.52

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