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- PDB-7obs: Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 7obs
TitleCrystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Receptor-interacting serine/threonine-protein kinase 2
KeywordsSIGNALING PROTEIN / 14-3-3 protein protein-peptide complex
Function / homology
Function and homology information


response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / positive regulation of cytokine-mediated signaling pathway / immature T cell proliferation in thymus / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / LIM domain binding / xenophagy / CD4-positive, alpha-beta T cell proliferation ...response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / positive regulation of cytokine-mediated signaling pathway / immature T cell proliferation in thymus / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / LIM domain binding / xenophagy / CD4-positive, alpha-beta T cell proliferation / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of protein K63-linked ubiquitination / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / positive regulation of immature T cell proliferation in thymus / caspase binding / JUN kinase kinase kinase activity / cellular response to peptidoglycan / response to interleukin-12 / positive regulation of CD4-positive, alpha-beta T cell proliferation / activation of cysteine-type endopeptidase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of macrophage cytokine production / toll-like receptor 4 signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / response to exogenous dsRNA / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / cellular response to lipoteichoic acid / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / canonical NF-kappaB signal transduction / establishment of skin barrier / positive regulation of interferon-alpha production / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signaling adaptor activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / stress-activated MAPK cascade / negative regulation of stem cell proliferation / positive regulation of chemokine production / RHO GTPases activate PKNs / JNK cascade / lipopolysaccharide-mediated signaling pathway / protein kinase A signaling / protein sequestering activity / p75NTR recruits signalling complexes / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / negative regulation of innate immune response / positive regulation of interferon-beta production / protein export from nucleus / response to interleukin-1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / 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 peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / stem cell proliferation / positive regulation of protein ubiquitination / activated TAK1 mediates p38 MAPK activation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / negative regulation of protein kinase activity / TAK1-dependent IKK and NF-kappa-B activation / non-membrane spanning protein tyrosine kinase activity / NOD1/2 Signaling Pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of interleukin-6 production / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of type II interferon production / Ovarian tumor domain proteases / Downstream TCR signaling / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of cell growth / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / vesicle / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / non-specific serine/threonine protein kinase / regulation of cell cycle
Similarity search - Function
Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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 ...Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 2 / 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 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Receptor-interacting serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6656
Polymers29,5522
Non-polymers1134
Water7,566420
1
A: 14-3-3 protein sigma
B: Receptor-interacting serine/threonine-protein kinase 2
hetero molecules

A: 14-3-3 protein sigma
B: Receptor-interacting serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,33012
Polymers59,1044
Non-polymers2268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.612, 111.816, 62.713
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-304-

MG

21A-784-

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 Receptor-interacting serine/threonine-protein kinase 2 / CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ...CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ICE-kinase / RIP-like-interacting CLARP kinase / Receptor-interacting protein 2 / RIP-2 / Tyrosine-protein kinase RIPK2


Mass: 1325.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O43353, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH7.7, 23%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→33.23 Å / Num. obs: 26678 / % possible obs: 98 % / Redundancy: 6.3 % / Biso Wilson estimate: 8.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1210 / CC1/2: 0.927 / % possible all: 90.6

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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→31.36 Å / SU ML: 0.1586 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9107 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1887 1406 5.27 %
Rwork0.146 25253 -
obs0.1483 26659 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 4 420 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362004
X-RAY DIFFRACTIONf_angle_d0.62762716
X-RAY DIFFRACTIONf_chiral_restr0.0337300
X-RAY DIFFRACTIONf_plane_restr0.0032358
X-RAY DIFFRACTIONf_dihedral_angle_d15.31481263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.2231200.17472333X-RAY DIFFRACTION92.15
1.87-1.940.19341280.16542419X-RAY DIFFRACTION94.44
1.94-2.030.20671310.15042447X-RAY DIFFRACTION95.91
2.03-2.140.18261310.13812476X-RAY DIFFRACTION97.57
2.14-2.270.19391290.13442565X-RAY DIFFRACTION99.63
2.27-2.450.17321560.13852538X-RAY DIFFRACTION100
2.45-2.690.20631370.14462592X-RAY DIFFRACTION100
2.69-3.080.18831500.14622570X-RAY DIFFRACTION100
3.08-3.880.16611680.12972609X-RAY DIFFRACTION100
3.88-31.360.19761560.16072704X-RAY DIFFRACTION99.83

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