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- PDB-8c28: 14-3-3 in complex with PyrinpS208pS242 -

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Basic information

Entry
Database: PDB / ID: 8c28
Title14-3-3 in complex with PyrinpS208pS242
Components
  • 14-3-3 protein sigma
  • Pyrin
KeywordsPROTEIN BINDING / protein-peptide interaction / phosphorylation reader protein / immunology / scaffolding / intrinsic disorder motif
Function / homology
Function and homology information


pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / canonical inflammasome complex / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production ...pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / canonical inflammasome complex / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / pyroptotic inflammatory response / response to type II interferon / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of cytokine production involved in inflammatory response / autophagosome / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of autophagy / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Purinergic signaling in leishmaniasis infection / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / ruffle / protein kinase A signaling / protein sequestering activity / 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 / positive regulation of interleukin-1 beta production / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of inflammatory response / positive regulation of inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin protein ligase activity / lamellipodium / actin binding / cytoplasmic vesicle / positive regulation of cell growth / regulation of gene expression / microtubule / regulation of cell cycle / protein ubiquitination / cadherin binding / inflammatory response / innate immune response / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
SPRY-associated domain / SPRY-associated / PRY / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger ...SPRY-associated domain / SPRY-associated / PRY / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / 14-3-3 protein sigma / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Pyrin / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLau, R. / Ottmann, C. / Hann, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 14-3-3/Pyrin complex
Authors: Ottmann, C. / Lau, R.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 14-3-3 protein sigma
BBB: 14-3-3 protein sigma
CCC: Pyrin
DDD: Pyrin
PPP: Pyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9216
Polymers67,6395
Non-polymers2821
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-26 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.443, 80.689, 142.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26558.914 Da / Num. of mol.: 2
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 Pyrin / Marenostrin


Mass: 4840.313 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15553
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.19 M CaCl 2 , 5% glycerol, 26% PEG 400, 0.095 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 96682 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.996 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4660 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.923 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.596 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.213 4865 5.037 %
Rwork0.1793 91711 -
all0.181 --
obs-96576 99.478 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.258 Å2
Baniso -1Baniso -2Baniso -3
1--1.163 Å20 Å20 Å2
2--3.305 Å2-0 Å2
3----2.142 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 19 564 4377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133936
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153718
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6485311
X-RAY DIFFRACTIONr_angle_other_deg1.5081.5848564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5065499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57521.805205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4881533
X-RAY DIFFRACTIONr_chiral_restr0.090.2510
X-RAY DIFFRACTIONr_chiral_restr_other0.0370.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02868
X-RAY DIFFRACTIONr_nbd_refined0.2170.2916
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.23388
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21969
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2442
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.29
X-RAY DIFFRACTIONr_nbd_other0.2970.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.227
X-RAY DIFFRACTIONr_mcbond_it3.1593.581987
X-RAY DIFFRACTIONr_mcbond_other3.1393.5781985
X-RAY DIFFRACTIONr_mcangle_it4.3775.3282483
X-RAY DIFFRACTIONr_mcangle_other4.3725.3282483
X-RAY DIFFRACTIONr_scbond_it4.6574.0091949
X-RAY DIFFRACTIONr_scbond_other4.6564.0091950
X-RAY DIFFRACTIONr_scangle_it6.8025.8412826
X-RAY DIFFRACTIONr_scangle_other6.8015.8422827
X-RAY DIFFRACTIONr_lrange_it8.39244.4854804
X-RAY DIFFRACTIONr_lrange_other8.23243.5164640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3393720.3366635X-RAY DIFFRACTION98.5098
1.642-1.6870.2863560.3096499X-RAY DIFFRACTION99.1753
1.687-1.7350.3373420.2986334X-RAY DIFFRACTION99.4044
1.735-1.7890.2773240.2646160X-RAY DIFFRACTION99.2348
1.789-1.8470.2593220.2335978X-RAY DIFFRACTION99.1814
1.847-1.9120.2972910.2345814X-RAY DIFFRACTION99.3814
1.912-1.9840.2622960.2295618X-RAY DIFFRACTION99.4451
1.984-2.0650.272620.1995438X-RAY DIFFRACTION99.6678
2.065-2.1570.2312930.1815163X-RAY DIFFRACTION99.5984
2.157-2.2620.2082620.1764974X-RAY DIFFRACTION99.5437
2.262-2.3840.2082530.1564746X-RAY DIFFRACTION99.681
2.384-2.5290.192320.1644500X-RAY DIFFRACTION99.621
2.529-2.7030.2342240.1744247X-RAY DIFFRACTION99.8883
2.703-2.9190.2392080.1713956X-RAY DIFFRACTION99.928
2.919-3.1980.1871810.1723679X-RAY DIFFRACTION99.8448
3.198-3.5740.2051650.1723343X-RAY DIFFRACTION99.8577
3.574-4.1250.1821690.1532934X-RAY DIFFRACTION99.9678
4.125-5.0480.1581420.1382532X-RAY DIFFRACTION99.9253
5.048-7.1210.2221180.1941978X-RAY DIFFRACTION99.8095
7.121-49.90.215530.1721183X-RAY DIFFRACTION99.5169

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