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- PDB-7obh: Crystal structure of 14-3-3 sigma in complex with NPM1 phosphopep... -

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Basic information

Entry
Database: PDB / ID: 7obh
TitleCrystal structure of 14-3-3 sigma in complex with NPM1 phosphopeptide and stabilizer Fusicoccin-A
Components
  • 14-3-3 protein sigma
  • NPM1 phosphopeptide
KeywordsSIGNALING PROTEIN / 14-3-3 sigma protein-peptide-Stabilizer complex
Function / homology
Function and homology information


regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / regulation of endoribonuclease activity / negative regulation of centrosome duplication / positive regulation of cell cycle G2/M phase transition / regulation of endodeoxyribonuclease activity / regulation of centriole replication / granular component / positive regulation of centrosome duplication / positive regulation of protein localization to nucleolus ...regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / regulation of endoribonuclease activity / negative regulation of centrosome duplication / positive regulation of cell cycle G2/M phase transition / regulation of endodeoxyribonuclease activity / regulation of centriole replication / granular component / positive regulation of centrosome duplication / positive regulation of protein localization to nucleolus / negative regulation of protein kinase activity by regulation of protein phosphorylation / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / SARS-CoV-1-host interactions / regulation of centrosome duplication / spindle pole centrosome / ALK mutants bind TKIs / Tat protein binding / Nuclear import of Rev protein / cell volume homeostasis / centrosome cycle / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of DNA damage response, signal transduction by p53 class mediator / nucleocytoplasmic transport / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / protein kinase inhibitor activity / regulation of cell-cell adhesion / ribosomal large subunit binding / negative regulation of mRNA splicing, via spliceosome / macrophage differentiation / cAMP/PKA signal transduction / ribosomal small subunit binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / ribosomal large subunit export from nucleus / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / NF-kappaB binding / 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 / core promoter sequence-specific DNA binding / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / Nuclear events stimulated by ALK signaling in cancer / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / ribosomal small subunit export from nucleus / positive regulation of protein localization / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of cell adhesion / SUMOylation of transcription cofactors / 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 translation / positive regulation of protein export from nucleus / ribosomal large subunit biogenesis / positive regulation of protein ubiquitination / stem cell proliferation / ribosome assembly / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / regulation of cell growth / positive regulation of NF-kappaB transcription factor activity / protein-DNA complex / PKR-mediated signaling / intrinsic apoptotic signaling pathway in response to DNA damage / protein import into nucleus / cellular response to UV / cellular senescence / Signaling by ALK fusions and activated point mutants / intracellular protein localization / unfolded protein binding / nucleosome assembly / large ribosomal subunit / regulation of protein localization / ribosomal small subunit biogenesis / positive regulation of cell growth / small ribosomal subunit / histone binding / molecular adaptor activity / DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / rRNA binding / protein stabilization / nuclear speck / cadherin binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation
Similarity search - Function
Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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
FUSICOCCIN / Nucleophosmin / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: NPM1 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4974
Polymers29,7812
Non-polymers7162
Water7,386410
1
A: 14-3-3 protein sigma
B: NPM1 phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
B: NPM1 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9958
Polymers59,5624
Non-polymers1,4334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6620 Å2
ΔGint-57 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.475, 112.195, 62.675
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-797-

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 NPM1 phosphopeptide / Nucleophosmin / NPM / Nucleolar phosphoprotein B23 / Nucleolar protein NO38 / Numatrin


Mass: 1554.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06748
#3: Chemical ChemComp-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12 / Feature type: SUBJECT OF INVESTIGATION
#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.: 410 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.3, 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 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2→33.23 Å / Num. obs: 19953 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 7.52 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.04 Å / Redundancy: 6 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 979 / CC1/2: 0.952 / % possible all: 99.7

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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: 2→33.23 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1015 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1804 996 5 %
Rwork0.1417 18942 -
obs0.1437 19938 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.52 Å2
Refinement stepCycle: LAST / Resolution: 2→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 49 410 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881991
X-RAY DIFFRACTIONf_angle_d1.03362697
X-RAY DIFFRACTIONf_chiral_restr0.0464303
X-RAY DIFFRACTIONf_plane_restr0.0061343
X-RAY DIFFRACTIONf_dihedral_angle_d14.58341202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.19551390.13782655X-RAY DIFFRACTION99.86
2.11-2.240.19721420.13432677X-RAY DIFFRACTION100
2.24-2.410.1991400.13522676X-RAY DIFFRACTION100
2.41-2.660.18531410.13962674X-RAY DIFFRACTION100
2.66-3.040.18991430.14292705X-RAY DIFFRACTION100
3.04-3.830.15531420.12962717X-RAY DIFFRACTION100
3.83-33.230.17191490.16392838X-RAY DIFFRACTION99.9

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