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- PDB-7obk: Crystal structure of 14-3-3 sigma in complex with PKR phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 7obk
TitleCrystal structure of 14-3-3 sigma in complex with PKR phosphopeptide
Components
  • 14-3-3 protein sigma
  • PKR phosphopeptide
KeywordsSIGNALING PROTEIN / 14-3-3 protein protein-peptide complex
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / negative regulation of osteoblast proliferation / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / negative regulation of osteoblast proliferation / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / 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 / 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 / positive regulation of protein localization / RHO GTPases activate PKNs / endoplasmic reticulum unfolded protein response / positive regulation of chemokine production / antiviral innate immune response / protein kinase A signaling / protein sequestering activity / protein export from nucleus / cellular response to amino acid starvation / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / positive regulation of cytokine production / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / non-specific protein-tyrosine kinase / negative regulation of protein kinase activity / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage / double-stranded RNA binding / Interferon alpha/beta signaling / protein localization / kinase activity / positive regulation of NF-kappaB transcription factor activity / regulation of protein localization / positive regulation of cell growth / defense response to virus / protein autophosphorylation / positive regulation of MAPK cascade / negative regulation of translation / regulation of cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / ribosome / cadherin binding / translation / protein phosphorylation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / 14-3-3 protein sigma / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / 14-3-3 protein sigma / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCentorrino, F. / Andlovic, B. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: Cell Chem Biol / Year: 2023
Title: IFN alpha primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization.
Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, ...Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, F. / Kaiser, M. / Eickhoff, J. / Ottmann, C.
History
DepositionApr 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: PKR phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7044
Polymers29,6552
Non-polymers492
Water7,963442
1
A: 14-3-3 protein sigma
B: PKR phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
B: PKR phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4078
Polymers59,3104
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.714, 112.560, 62.623
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

21A-820-

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 BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide PKR phosphopeptide / Interferon-induced / double-stranded RNA-activated protein kinase / Eukaryotic translation ...Interferon-induced / double-stranded RNA-activated protein kinase / Eukaryotic translation initiation factor 2-alpha kinase 2 / eIF-2A protein kinase 2 / Interferon-inducible RNA-dependent protein kinase / P1/eIF-2A protein kinase / Protein kinase RNA-activated / PKR / Protein kinase R / Tyrosine-protein kinase EIF2AK2 / p68 kinase


Mass: 1428.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH7.3, 25%PEG 400, 0.19 M CaCl2 and 5 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.8→41.87 Å / Num. obs: 27306 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 8.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1311 / CC1/2: 0.921 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.8→41.86 Å / SU ML: 0.1522 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 16.1356 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.183 1365 5 %
Rwork0.1453 25923 -
obs0.1472 27288 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 2 442 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092029
X-RAY DIFFRACTIONf_angle_d0.94712748
X-RAY DIFFRACTIONf_chiral_restr0.0464301
X-RAY DIFFRACTIONf_plane_restr0.0061364
X-RAY DIFFRACTIONf_dihedral_angle_d16.06871264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.2211330.17962521X-RAY DIFFRACTION98.66
1.87-1.940.21891340.16142555X-RAY DIFFRACTION99.48
1.94-2.030.16991340.14552553X-RAY DIFFRACTION99.52
2.03-2.140.16431340.1372537X-RAY DIFFRACTION99.37
2.14-2.270.16871370.12992589X-RAY DIFFRACTION100
2.27-2.450.19631350.13472582X-RAY DIFFRACTION100
2.45-2.690.16681380.13892610X-RAY DIFFRACTION100
2.69-3.080.19521360.142593X-RAY DIFFRACTION100
3.08-3.880.15741400.13472650X-RAY DIFFRACTION100
3.88-41.860.20261440.1652733X-RAY DIFFRACTION99.86

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