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- PDB-6y40: 14-3-3 Sigma in complex with phosphorylated PLN peptide -

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Basic information

Entry
Database: PDB / ID: 6y40
Title14-3-3 Sigma in complex with phosphorylated PLN peptide
Components
  • 14-3-3 protein sigma
  • PLN peptide
KeywordsPROTEIN BINDING / 14-3-3 / PLN / complex / protein / protein-protein interactions
Function / homology
Function and homology information


regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of cardiac muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / negative regulation of calcium ion transmembrane transporter activity ...regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of cardiac muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly / negative regulation of calcium ion import / negative regulation of catalytic activity / ATPase inhibitor activity / regulation of the force of heart contraction / negative regulation of ATP-dependent activity / cardiac muscle tissue development / regulation of cardiac muscle cell contraction / blood circulation / enzyme inhibitor activity / regulation of heart contraction / relaxation of cardiac muscle / negative regulation of heart rate / muscle cell cellular homeostasis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of calcium ion transport / Ion transport by P-type ATPases / negative regulation of calcium ion transport / 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 / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / 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 / RHO GTPases activate PKNs / Ion homeostasis / Notch signaling pathway / protein kinase A signaling / sarcoplasmic reticulum membrane / regulation of cytosolic calcium ion concentration / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / sarcoplasmic reticulum / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intracellular calcium ion homeostasis / intrinsic apoptotic signaling pathway in response to DNA damage / ATPase binding / positive regulation of cell growth / regulation of cell cycle / cadherin binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / protein homodimerization activity / mitochondrion / extracellular space / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Phospholamban / Phospholamban / 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
Similarity search - Domain/homology
Cardiac phospholamban / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBallone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675179 Netherlands
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes.
Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Apr 28, 2021Group: Data collection / Category: reflns / Item: _reflns.pdbx_redundancy
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: PLN peptide
A: 14-3-3 protein sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2836
Polymers30,1752
Non-polymers1084
Water9,314517
1
P: PLN peptide
A: 14-3-3 protein sigma
hetero molecules

P: PLN peptide
A: 14-3-3 protein sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56612
Polymers60,3494
Non-polymers2178
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.300, 112.390, 62.569
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-303-

MG

21A-753-

HOH

31A-883-

HOH

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Components

#1: Protein/peptide PLN peptide


Mass: 1948.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P26678*PLUS
#2: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28226.518 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
#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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400, 1.25% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.59→41.81 Å / Num. obs: 31591 / % possible obs: 80.2 % / Biso Wilson estimate: 9.62 Å2 / CC1/2: 0.996 / Net I/σ(I): 14.3
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 31591 / CC1/2: 0.937 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
REFMAC5.5refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.75→41.81 Å / SU ML: 0.1565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4398
RfactorNum. reflection% reflection
Rfree0.207 1389 4.88 %
Rwork0.168 --
obs0.1699 28454 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.59 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 4 517 2353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652021
X-RAY DIFFRACTIONf_angle_d0.75292771
X-RAY DIFFRACTIONf_chiral_restr0.0407317
X-RAY DIFFRACTIONf_plane_restr0.0045360
X-RAY DIFFRACTIONf_dihedral_angle_d4.54482021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.26411120.21222062X-RAY DIFFRACTION74.3
1.81-1.890.23991340.18762704X-RAY DIFFRACTION96.46
1.89-1.970.21941390.16332697X-RAY DIFFRACTION97.86
1.97-2.070.1831270.15972774X-RAY DIFFRACTION98.17
2.07-2.20.22761480.15952720X-RAY DIFFRACTION98.19
2.2-2.380.19751380.16292740X-RAY DIFFRACTION98.02
2.38-2.610.18751620.16342756X-RAY DIFFRACTION98.32
2.61-2.990.21881270.17172822X-RAY DIFFRACTION98.86
2.99-3.770.19921670.15532826X-RAY DIFFRACTION99.77
3.77-41.810.19951350.17752964X-RAY DIFFRACTION99.3

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