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- PDB-8c2d: 14-3-3 in complex with Pyrin pS208 -

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Basic information

Entry
Database: PDB / ID: 8c2d
Title14-3-3 in complex with Pyrin pS208
Components
  • 14-3-3 protein sigma
  • Pyrin pS208 peptide
KeywordsPROTEIN BINDING / protein-peptide interaction / phosphorylation reader protein / immunology / scaffolding / intrinsic disorder motif
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / 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 / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / 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 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
14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLau, R. / Ottmann, C. / Hann, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure and ligandability of the 14-3-3/pyrin interface.
Authors: Lau, R. / Hann, M.M. / Ottmann, C.
#1: Journal: Clin Genet / Year: 1987
Title: Effect of screening for cystic fibrosis on the influence of genetic counseling.
Authors: Dankert-Roelse, J.E. / te Meerman, G.J. / Knol, K. / ten Kate, L.P.
History
DepositionDec 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
AAA: 14-3-3 protein sigma
PPP: Pyrin pS208 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6516
Polymers28,5542
Non-polymers974
Water4,612256
1
AAA: 14-3-3 protein sigma
PPP: Pyrin pS208 peptide
hetero molecules

AAA: 14-3-3 protein sigma
PPP: Pyrin pS208 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,30312
Polymers57,1084
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5900 Å2
ΔGint-35 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.959, 111.538, 62.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-302-

MG

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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.: 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 Pyrin pS208 peptide


Mass: 1995.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.19 M CaCl2, 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→41.66 Å / Num. obs: 15990 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.999 / Net I/σ(I): 27
Reflection shellResolution: 2.15→2.15 Å / Mean I/σ(I) obs: 15.6 / Num. unique obs: 1162 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→41.659 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.11 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2099 860 5.383 %
Rwork0.1587 15115 -
all0.161 --
obs-15975 99.856 %
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: 19.066 Å2
Baniso -1Baniso -2Baniso -3
1-0.627 Å20 Å20 Å2
2--0.123 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 4 256 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131946
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171813
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6452624
X-RAY DIFFRACTIONr_angle_other_deg1.4471.5814202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3025248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69222105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.115358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8481516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_nbd_refined0.210.2416
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.21600
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2177
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.220
X-RAY DIFFRACTIONr_nbd_other0.1440.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.224
X-RAY DIFFRACTIONr_mcbond_it1.9881.88986
X-RAY DIFFRACTIONr_mcbond_other1.9861.876985
X-RAY DIFFRACTIONr_mcangle_it3.1772.7921233
X-RAY DIFFRACTIONr_mcangle_other3.1772.7961234
X-RAY DIFFRACTIONr_scbond_it2.5332.063960
X-RAY DIFFRACTIONr_scbond_other2.5312.06958
X-RAY DIFFRACTIONr_scangle_it4.0482.9891390
X-RAY DIFFRACTIONr_scangle_other4.0492.9891390
X-RAY DIFFRACTIONr_lrange_it5.99122.2832327
X-RAY DIFFRACTIONr_lrange_other5.95622.1612318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.15-2.2050.241520.16510920.16911560.9330.94998.96190.145
2.205-2.2660.25570.1810630.18311240.9180.94199.64410.169
2.266-2.3310.189620.15610610.15811260.9540.9599.73360.137
2.331-2.4030.257670.149860.14610530.9340.9651000.125
2.403-2.4810.239420.1449990.14710410.9380.9591000.129
2.481-2.5680.196630.1339450.13710080.950.9691000.12
2.568-2.6650.188480.1459430.1479910.9550.9631000.132
2.665-2.7730.222720.1448460.159180.9440.9621000.132
2.773-2.8960.22480.1538490.1578970.9580.9611000.144
2.896-3.0360.176440.1518310.1528750.9610.9621000.143
3.036-3.1990.16350.1477780.1478130.9580.9711000.142
3.199-3.3920.229420.1587410.1627830.9530.9641000.156
3.392-3.6250.185400.1587000.1597400.9580.9661000.159
3.625-3.9130.183330.1596640.1616970.9580.9691000.161
3.913-4.2820.218320.1496070.1526390.9540.9691000.155
4.282-4.7820.156340.1475420.1485760.970.9721000.155
4.782-5.5090.194270.1895000.1895270.9450.9521000.198
5.509-6.7180.273280.2244150.2284430.9210.9221000.223
6.718-9.380.278180.1723450.1763630.9230.9661000.183
9.38-41.6590.251160.2262080.2282250.9480.94999.55560.232

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