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- PDB-6zcj: 14-3-3sigma in complex with SLP76pS376 phosphopeptide crystal str... -

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Basic information

Entry
Database: PDB / ID: 6zcj
Title14-3-3sigma in complex with SLP76pS376 phosphopeptide crystal structure
Components
  • 14-3-3 protein sigma
  • SLP76pS376
KeywordsPEPTIDE BINDING PROTEIN / Adaptor Protein / Phosphorylation
Function / homology
Function and homology information


TCR signalosome / mast cell activation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / positive regulation of protein kinase activity / Generation of second messenger molecules ...TCR signalosome / mast cell activation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / positive regulation of protein kinase activity / Generation of second messenger molecules / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / plasma membrane raft / keratinocyte proliferation / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / 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 / GPVI-mediated activation cascade / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / FCERI mediated Ca+2 mobilization / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / cell surface receptor protein tyrosine kinase signaling pathway / 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 / FCERI mediated MAPK activation / intrinsic apoptotic signaling pathway in response to DNA damage / cell-cell junction / intracellular protein localization / DAP12 signaling / T cell receptor signaling pathway / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / intracellular signal transduction / immune response / 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 / SAM domain (Sterile alpha motif) / 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 / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / SAM domain (Sterile alpha motif) / 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 / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Lymphocyte cytosolic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsSoini, L. / Leysen, S. / Davis, J. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission675179 Netherlands
CitationJournal: Febs Lett. / Year: 2021
Title: The 14-3-3/SLP76 protein-protein interaction in T-cell receptor signalling: a structural and biophysical characterization.
Authors: Soini, L. / Leysen, S. / Davis, J. / Westwood, M. / Ottmann, C.
History
DepositionJun 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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 1.3Nov 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: SLP76pS376
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8517
Polymers27,7292
Non-polymers1225
Water5,657314
1
A: 14-3-3 protein sigma
P: SLP76pS376
hetero molecules

A: 14-3-3 protein sigma
P: SLP76pS376
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,70114
Polymers55,4584
Non-polymers24310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4850 Å2
ΔGint-50 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.098, 111.876, 62.400
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

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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 SLP76pS376


Mass: 1186.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q13094*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
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: 0.69 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.69 Å / Relative weight: 1
ReflectionResolution: 1.53→66.19 Å / Num. obs: 43290 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.1
Reflection shellResolution: 1.53→1.56 Å / Rmerge(I) obs: 0.43 / Num. unique obs: 1922 / CC1/2: 0.78

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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: 1.53→45.4 Å / SU ML: 0.1486 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 2156 4.98 %
Rwork0.1682 41107 -
obs0.1692 43263 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.99 Å2
Refinement stepCycle: LAST / Resolution: 1.53→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 5 314 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832089
X-RAY DIFFRACTIONf_angle_d0.92232836
X-RAY DIFFRACTIONf_chiral_restr0.0504309
X-RAY DIFFRACTIONf_plane_restr0.0051371
X-RAY DIFFRACTIONf_dihedral_angle_d19.4291834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.28931240.26062471X-RAY DIFFRACTION90.61
1.57-1.60.25221400.23012638X-RAY DIFFRACTION96.19
1.6-1.650.2441390.20662699X-RAY DIFFRACTION98.99
1.65-1.70.21161490.18322750X-RAY DIFFRACTION99.86
1.7-1.750.2351310.18422735X-RAY DIFFRACTION99.97
1.75-1.810.22741590.18362714X-RAY DIFFRACTION99.93
1.81-1.890.22581540.17272737X-RAY DIFFRACTION100
1.89-1.970.16691520.16512745X-RAY DIFFRACTION99.97
1.97-2.080.19691560.16482757X-RAY DIFFRACTION99.97
2.08-2.210.19521570.16162726X-RAY DIFFRACTION100
2.21-2.380.19181330.15862783X-RAY DIFFRACTION100
2.38-2.620.17941510.16442778X-RAY DIFFRACTION99.97
2.62-2.990.17151230.17242811X-RAY DIFFRACTION100
2.99-3.770.1821270.15852833X-RAY DIFFRACTION99.97
3.77-45.40.17931610.16322930X-RAY DIFFRACTION99.87

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