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- PDB-7or3: Ternary complex of 14-3-3 sigma, NotchpS1917 phosphopeptide, and WQ136 -

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Basic information

Entry
Database: PDB / ID: 7or3
TitleTernary complex of 14-3-3 sigma, NotchpS1917 phosphopeptide, and WQ136
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-0AW / 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 1.0Jun 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 1.2Nov 13, 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)30,7537
Polymers29,5612
Non-polymers1,1925
Water5,332296
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)61,50614
Polymers59,1224
Non-polymers2,38410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area4880 Å2
ΔGint-52 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.458, 111.313, 62.169
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-412-

HOH

21A-683-

HOH

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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, 301 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-0AW / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-2,3-dihydro-1-benzofuran-5-carboxamide


Mass: 377.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
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 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→66.26 Å / Num. obs: 23871 / % possible obs: 88.7 % / Redundancy: 3 % / Biso Wilson estimate: 8.99 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1135 / CC1/2: 0.967 / % possible all: 83.7

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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: 1.8→66.26 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9309 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2468 1193 5 %
Rwork0.2223 22666 -
obs0.2236 23859 88.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→66.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 83 296 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111964
X-RAY DIFFRACTIONf_angle_d0.93032651
X-RAY DIFFRACTIONf_chiral_restr0.0469281
X-RAY DIFFRACTIONf_plane_restr0.0061341
X-RAY DIFFRACTIONf_dihedral_angle_d22.12571181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.31681260.29892401X-RAY DIFFRACTION84.94
1.87-1.960.35611300.31612476X-RAY DIFFRACTION89.15
1.96-2.060.2851080.26682064X-RAY DIFFRACTION73.13
2.06-2.190.30051230.28312342X-RAY DIFFRACTION83.82
2.19-2.360.2761290.23782448X-RAY DIFFRACTION87.03
2.36-2.60.23961400.19642651X-RAY DIFFRACTION93.5
2.6-2.970.23751410.19662682X-RAY DIFFRACTION94.16
2.97-3.740.17391450.17392750X-RAY DIFFRACTION95.54
3.74-66.260.21181510.19162852X-RAY DIFFRACTION95.76

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