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- PDB-7orh: Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ178 -

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Basic information

Entry
Database: PDB / ID: 7orh
TitleTernary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ178
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 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 ...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 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / ubiquitin ligase activator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / RHO GTPases activate CIT / nuclear export / negative regulation of mitotic cell cycle / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / cellular response to antibiotic / molecular function inhibitor activity / Cul4A-RING E3 ubiquitin ligase complex / 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 / Constitutive Signaling by AKT1 E17K in Cancer / PTK6 Regulates Cell Cycle / protein kinase inhibitor activity / regulation of cell-cell adhesion / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / inner ear development / regulation of G1/S transition of mitotic cell cycle / negative regulation of vascular associated smooth muscle cell proliferation / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / 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 / 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 / Cyclin E associated events during G1/S transition / negative regulation of protein kinase activity / 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 / positive regulation of cell adhesion / cyclin binding / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / regulation of cell migration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / placenta development / positive regulation of protein export from nucleus / positive regulation of DNA replication / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / G1/S transition of mitotic cell cycle / negative regulation of cell growth / DNA Damage/Telomere Stress Induced Senescence / potassium ion transport / SCF(Skp2)-mediated degradation of p27/p21 / intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of epithelial cell proliferation / positive regulation of protein catabolic process / Cyclin D associated events in G1 / cellular senescence / intracellular protein localization / regulation of protein localization / protein-folding chaperone binding / heart development / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / molecular adaptor activity / regulation of cell cycle / endosome / cilium / ciliary basal body / cadherin binding
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-0B7 / 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 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

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)30,5827
Polymers29,7492
Non-polymers8335
Water5,296294
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)61,16414
Polymers59,4984
Non-polymers1,66610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.428, 111.483, 62.261
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-678-

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, 299 molecules

#3: Chemical ChemComp-0B7 / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-1~{H}-indole-6-carboxamide


Mass: 374.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18N4OS / 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.: 294 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
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 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→41.53 Å / Num. obs: 26790 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1291 / CC1/2: 0.874 / % possible all: 95.8

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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→41.53 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0666 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2133 1338 5 %
Rwork0.1767 25435 -
obs0.1784 26773 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 57 294 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891978
X-RAY DIFFRACTIONf_angle_d0.98242682
X-RAY DIFFRACTIONf_chiral_restr0.0471289
X-RAY DIFFRACTIONf_plane_restr0.0063348
X-RAY DIFFRACTIONf_dihedral_angle_d16.19441216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.24321300.21422461X-RAY DIFFRACTION97.7
1.87-1.940.25591310.22509X-RAY DIFFRACTION99.51
1.94-2.030.20361330.19082511X-RAY DIFFRACTION99.77
2.03-2.140.21331310.1722507X-RAY DIFFRACTION99.85
2.14-2.270.24721340.16912534X-RAY DIFFRACTION100
2.27-2.450.20611340.16262535X-RAY DIFFRACTION99.96
2.45-2.690.18741340.17272537X-RAY DIFFRACTION100
2.69-3.080.22431340.17772560X-RAY DIFFRACTION100
3.08-3.880.181360.16222597X-RAY DIFFRACTION100
3.88-41.530.22761410.18342684X-RAY DIFFRACTION99.93

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