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- PDB-6y8b: 14-3-3 Sigma in complex with phosphorylated caspase{pS139} peptide -

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Basic information

Entry
Database: PDB / ID: 6y8b
Title14-3-3 Sigma in complex with phosphorylated caspase{pS139} peptide
Components
  • 14-3-3 protein sigma
  • TYR-ASP-LEU-SEP-LEU-PRO-PHE-PRO
KeywordsPROTEIN BINDING / 14-3-3 / caspase{pS139} / complex / protein / protein-protein interactions
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / regulation of epidermal cell division / protein kinase C inhibitor activity ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / TP53 Regulates Transcription of Caspase Activators and Caspases / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / ectopic germ cell programmed cell death / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / extrinsic apoptotic signaling pathway in absence of ligand / protein kinase A signaling / protein sequestering activity / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / negative regulation of protein kinase activity / NOD1/2 Signaling Pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein processing / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / positive regulation of cell growth / regulation of cell cycle / cadherin binding / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / nucleolus / negative regulation of apoptotic process / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Caspase-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / 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 / Death-like domain superfamily
Similarity search - Domain/homology
14-3-3 protein sigma / Caspase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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
DepositionMar 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: TYR-ASP-LEU-SEP-LEU-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3666
Polymers29,2582
Non-polymers1084
Water6,557364
1
A: 14-3-3 protein sigma
P: TYR-ASP-LEU-SEP-LEU-PRO-PHE-PRO
hetero molecules

A: 14-3-3 protein sigma
P: TYR-ASP-LEU-SEP-LEU-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,73212
Polymers58,5154
Non-polymers2178
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5260 Å2
ΔGint-78 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.797, 112.964, 62.446
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-749-

HOH

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Components

#1: 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
#2: Protein/peptide TYR-ASP-LEU-SEP-LEU-PRO-PHE-PRO


Mass: 1031.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42575*PLUS
#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


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


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 28% PEG400, 5% 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.973 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: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.54→30.05 Å / Num. obs: 42300 / % possible obs: 97.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.996 / Net I/σ(I): 14.3
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 1084 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
REFMACV5.5refinement
PHENIX1.16_3549refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.54→30.05 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5285
RfactorNum. reflection% reflection
Rfree0.2121 2083 5.01 %
Rwork0.1796 --
obs0.1812 41586 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.87 Å2
Refinement stepCycle: LAST / Resolution: 1.54→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 4 364 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551968
X-RAY DIFFRACTIONf_angle_d0.76172692
X-RAY DIFFRACTIONf_chiral_restr0.0412304
X-RAY DIFFRACTIONf_plane_restr0.0049353
X-RAY DIFFRACTIONf_dihedral_angle_d5.12661620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.3893910.30031670X-RAY DIFFRACTION62.14
1.58-1.620.25211370.24012615X-RAY DIFFRACTION96.49
1.62-1.660.24931450.21692625X-RAY DIFFRACTION96.45
1.66-1.710.29071370.2112633X-RAY DIFFRACTION97.78
1.71-1.770.22431430.20282657X-RAY DIFFRACTION97.63
1.77-1.830.2271400.19262662X-RAY DIFFRACTION98.01
1.83-1.90.22711380.18452662X-RAY DIFFRACTION98.07
1.9-1.990.22281420.18692682X-RAY DIFFRACTION98.47
1.99-2.10.24051500.182680X-RAY DIFFRACTION99.12
2.1-2.230.22661530.1742714X-RAY DIFFRACTION99.07
2.23-2.40.20461550.17182699X-RAY DIFFRACTION99.27
2.4-2.640.1971430.17562730X-RAY DIFFRACTION99.45
2.64-3.020.19111370.17612763X-RAY DIFFRACTION99.28
3.02-3.810.20791320.16362791X-RAY DIFFRACTION99.83
3.81-30.050.18071400.16922920X-RAY DIFFRACTION99.8

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