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- PDB-7org: Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ162 -

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Basic information

Entry
Database: PDB / ID: 7org
TitleTernary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ162
Components
  • 14-3-3 protein sigma
  • Cyclin-dependent kinase inhibitor 1B
KeywordsSIGNALING PROTEIN / protein-peptide complex small-molecule
Function / homology
Function and homology information


cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of phosphorylation / negative regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of cyclin-dependent protein serine/threonine kinase activity ...cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of phosphorylation / negative regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / negative regulation of epithelial cell apoptotic process / epithelial cell proliferation involved in prostate gland development / ubiquitin ligase activator activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / RHO GTPases activate CIT / nuclear export / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to antibiotic / Cul4A-RING E3 ubiquitin ligase complex / molecular function inhibitor activity / cellular response to lithium ion / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / p53-Dependent G1 DNA Damage Response / protein kinase inhibitor activity / PTK6 Regulates Cell Cycle / Constitutive Signaling by AKT1 E17K in Cancer / regulation of cell-cell adhesion / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / : / inner ear development / regulation of G1/S transition of mitotic cell cycle / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / negative regulation of mitotic cell cycle / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / response to amino acid / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / response to glucose / Cyclin E associated events during G1/S transition / response to cadmium ion / negative regulation of stem cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / Notch signaling pathway / positive regulation of microtubule polymerization / FLT3 Signaling / Hsp70 protein binding / positive regulation of cell adhesion / protein sequestering activity / cyclin binding / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of cell migration / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / positive regulation of DNA replication / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / placenta development / sensory perception of sound / potassium ion transport / negative regulation of cell growth / DNA Damage/Telomere Stress Induced Senescence / response to peptide hormone / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of protein catabolic process / negative regulation of epithelial cell proliferation / Cyclin D associated events in G1 / cellular senescence / intracellular protein localization / response to estradiol / regulation of protein localization / protein-folding chaperone binding / heart development / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP)
Similarity search - Function
Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / 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 ...Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / 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
Chem-09W / 14-3-3 protein sigma / Cyclin-dependent kinase inhibitor 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCentorrino, F. / Wu, Q. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: To Be Published
Title: A crystallography-based study of fragment extensions into the 14-3-3 binding groove
Authors: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / Ottmann, C.
History
DepositionJun 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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
P: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5887
Polymers29,7492
Non-polymers8395
Water5,657314
1
A: 14-3-3 protein sigma
P: Cyclin-dependent kinase inhibitor 1B
hetero molecules

A: 14-3-3 protein sigma
P: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,17614
Polymers59,4984
Non-polymers1,67810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.607, 110.882, 61.152
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-702-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#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 Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinase inhibitor p27 / p27Kip1


Mass: 1522.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P46527

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Non-polymers , 4 types, 319 molecules

#3: Chemical ChemComp-09W / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-2,3-dihydro-1-benzofuran-7-carboxamide


Mass: 377.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH7.3, 26%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: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→41.07 Å / Num. obs: 25796 / % possible obs: 98.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1183 / CC1/2: 0.951 / % possible all: 91.8

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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→41.07 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1187 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2022 1289 5 %
Rwork0.1597 24496 -
obs0.1618 25785 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 57 314 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951975
X-RAY DIFFRACTIONf_angle_d1.10422682
X-RAY DIFFRACTIONf_chiral_restr0.0463292
X-RAY DIFFRACTIONf_plane_restr0.0062350
X-RAY DIFFRACTIONf_dihedral_angle_d17.72651216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.25981340.19912554X-RAY DIFFRACTION93.37
1.87-1.960.22551390.17252630X-RAY DIFFRACTION96.08
1.96-2.060.1831400.15962662X-RAY DIFFRACTION97.29
2.06-2.190.23031410.15492693X-RAY DIFFRACTION97.62
2.19-2.360.20971430.14662719X-RAY DIFFRACTION98.93
2.36-2.60.20791450.15262743X-RAY DIFFRACTION99.38
2.6-2.980.16921460.15242778X-RAY DIFFRACTION99.59
2.98-3.750.16971460.1472794X-RAY DIFFRACTION99.97
3.75-41.070.22031550.17372923X-RAY DIFFRACTION99.87

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