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- PDB-7or7: Ternary complex of 14-3-3 sigma, NotchpS1917 phosphopeptide, and WQ178 -

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Basic information

Entry
Database: PDB / ID: 7or7
TitleTernary complex of 14-3-3 sigma, NotchpS1917 phosphopeptide, and WQ178
Components
  • 14-3-3 protein sigma
  • Neurogenic locus notch homolog protein 4
KeywordsSIGNALING PROTEIN / protein-peptide complex small-molecule
Function / homology
Function and homology information


morphogenesis of a branching structure / negative regulation of endothelial cell differentiation / Defective LFNG causes SCDO3 / Pre-NOTCH Processing in the Endoplasmic Reticulum / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / negative regulation of cell adhesion molecule production / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / endothelial cell morphogenesis ...morphogenesis of a branching structure / negative regulation of endothelial cell differentiation / Defective LFNG causes SCDO3 / Pre-NOTCH Processing in the Endoplasmic Reticulum / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / negative regulation of cell adhesion molecule production / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / endothelial cell morphogenesis / luteolysis / cell fate determination / negative regulation of cell-cell adhesion mediated by cadherin / mammary gland development / vasculature development / Notch binding / NOTCH4 Intracellular Domain Regulates Transcription / branching involved in blood vessel morphogenesis / Notch-HLH transcription pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / hemopoiesis / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / epithelial to mesenchymal transition / negative regulation of cell differentiation / 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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / cis-regulatory region sequence-specific DNA binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / 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 protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Negative regulation of NOTCH4 signaling / Pre-NOTCH Transcription and Translation / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / signaling receptor activity / regulation of protein localization / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / regulation of cell cycle / cadherin binding / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Neurogenic locus Notch 4 / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily ...Neurogenic locus Notch 4 / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR domain / LNR (Lin-12/Notch) repeat profile. / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / 14-3-3 protein sigma / EGF-like 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 / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-0B7 / 14-3-3 protein sigma / Neurogenic locus notch homolog protein 4
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 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 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
B: Neurogenic locus notch homolog protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9955
Polymers29,5612
Non-polymers4343
Water6,197344
1
A: 14-3-3 protein sigma
B: Neurogenic locus notch homolog protein 4
hetero molecules

A: 14-3-3 protein sigma
B: Neurogenic locus notch homolog protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,99010
Polymers59,1224
Non-polymers8686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4520 Å2
ΔGint-39 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.437, 111.431, 62.424
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-302-

MG

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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 Neurogenic locus notch homolog protein 4 / Notch 4 / hNotch4


Mass: 1334.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99466

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Non-polymers , 4 types, 347 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-0B7 / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-1~{H}-indole-6-carboxamide


Mass: 374.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N4OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH7.7, 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 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→41.57 Å / Num. obs: 26867 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 12.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1286 / CC1/2: 0.965 / % possible all: 94.4

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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→41.57 Å / SU ML: 0.1691 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2087 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1969 1343 5 %
Rwork0.1606 25506 -
obs0.1625 26849 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 29 344 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981920
X-RAY DIFFRACTIONf_angle_d1.18012594
X-RAY DIFFRACTIONf_chiral_restr0.0462283
X-RAY DIFFRACTIONf_plane_restr0.0062338
X-RAY DIFFRACTIONf_dihedral_angle_d20.32661166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.18771300.18062468X-RAY DIFFRACTION97.12
1.87-1.940.21271320.16452511X-RAY DIFFRACTION100
1.94-2.030.23411330.15742537X-RAY DIFFRACTION100
2.03-2.140.1861330.15572513X-RAY DIFFRACTION100
2.14-2.270.21511350.15052550X-RAY DIFFRACTION100
2.27-2.450.19891320.15132531X-RAY DIFFRACTION99.89
2.45-2.690.17671340.15872543X-RAY DIFFRACTION99.89
2.69-3.080.21671350.16182567X-RAY DIFFRACTION100
3.08-3.880.17541370.15162600X-RAY DIFFRACTION100
3.88-41.570.19721420.17552686X-RAY DIFFRACTION99.54

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