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- PDB-7oqj: Ternary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ162 -

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Basic information

Entry
Database: PDB / ID: 7oqj
TitleTernary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ162
Components
  • 14-3-3 protein sigma
  • Amot-p130 phosphopeptide (pS175)
KeywordsSIGNALING PROTEIN / protein-peptide complex small-molecule
Function / homology
Function and homology information


establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / positive regulation of embryonic development / Regulation of CDH11 function / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / gastrulation with mouth forming second ...establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / positive regulation of embryonic development / Regulation of CDH11 function / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability / cell-cell junction assembly / Signaling by Hippo / regulation of small GTPase mediated signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / endocytic vesicle / phosphoserine residue binding / positive regulation of blood vessel endothelial cell migration / Activation of BAD and translocation to mitochondria / positive regulation of cell size / negative regulation of keratinocyte proliferation / bicellular tight junction / establishment of skin barrier / negative regulation of protein localization to plasma membrane / vasculogenesis / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / stress fiber / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of stress fiber assembly / ruffle / protein sequestering activity / positive regulation of cell adhesion / negative regulation of innate immune response / release of cytochrome c from mitochondria / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of cell migration / negative regulation of angiogenesis / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / chemotaxis / cell junction / protein localization / lamellipodium / signaling receptor activity / regulation of protein localization / actin cytoskeleton organization / positive regulation of cell growth / cytoplasmic vesicle / angiogenesis / in utero embryonic development / regulation of cell cycle / postsynaptic density / cadherin binding / external side of plasma membrane / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / 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 ...Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / 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 / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCentorrino, F. / 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 3, 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 6, 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: Amot-p130 phosphopeptide (pS175)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0216
Polymers29,8532
Non-polymers1,1684
Water4,990277
1
A: 14-3-3 protein sigma
P: Amot-p130 phosphopeptide (pS175)
hetero molecules

A: 14-3-3 protein sigma
P: Amot-p130 phosphopeptide (pS175)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,04212
Polymers59,7074
Non-polymers2,3368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4600 Å2
ΔGint-45 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.815, 110.747, 61.940
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-405-

HOH

21A-660-

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 Amot-p130 phosphopeptide (pS175) / Angiomotin


Mass: 1626.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5
#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.: 3 / Source method: obtained synthetically / Formula: C21H19N3O2S / 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.: 277 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.095 M Hepes pH 7.5, 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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.4→61.94 Å / Num. obs: 56362 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.067 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2758 / CC1/2: 0.714 / Rpim(I) all: 1.019 / % possible all: 100

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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: 1.4→55.37 Å / SU ML: 0.1581 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.2471 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2009 3842 3.55 %
Rwork0.1778 104526 -
obs0.1786 56339 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→55.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 82 277 2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811956
X-RAY DIFFRACTIONf_angle_d0.97922648
X-RAY DIFFRACTIONf_chiral_restr0.0604283
X-RAY DIFFRACTIONf_plane_restr0.0055342
X-RAY DIFFRACTIONf_dihedral_angle_d20.0833731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.33341430.31953869X-RAY DIFFRACTION99.68
1.42-1.440.2981470.2983902X-RAY DIFFRACTION99.8
1.44-1.460.29451390.27883859X-RAY DIFFRACTION99.9
1.46-1.480.3171430.25443911X-RAY DIFFRACTION99.83
1.48-1.50.26991410.24193845X-RAY DIFFRACTION99.85
1.5-1.520.25251390.23543843X-RAY DIFFRACTION99.9
1.52-1.550.25251400.23193890X-RAY DIFFRACTION99.93
1.55-1.570.25621400.22323851X-RAY DIFFRACTION99.82
1.57-1.60.24411460.21413874X-RAY DIFFRACTION99.8
1.6-1.630.23071420.20953838X-RAY DIFFRACTION99.92
1.63-1.670.22931380.20473879X-RAY DIFFRACTION99.8
1.67-1.70.26511410.20383868X-RAY DIFFRACTION99.95
1.7-1.740.24071450.19393857X-RAY DIFFRACTION99.95
1.74-1.790.23641430.20063915X-RAY DIFFRACTION100
1.79-1.830.21451380.18213824X-RAY DIFFRACTION99.85
1.83-1.890.23831410.18493904X-RAY DIFFRACTION99.9
1.89-1.950.19111440.17463848X-RAY DIFFRACTION100
1.95-2.020.1791410.17513900X-RAY DIFFRACTION100
2.02-2.10.19781410.16613856X-RAY DIFFRACTION100
2.1-2.20.18651400.15713895X-RAY DIFFRACTION100
2.2-2.310.16741480.15863844X-RAY DIFFRACTION99.97
2.31-2.460.16791420.15013887X-RAY DIFFRACTION100
2.46-2.650.18881480.15283877X-RAY DIFFRACTION100
2.65-2.910.19361430.16233853X-RAY DIFFRACTION100
2.91-3.330.16551440.16013879X-RAY DIFFRACTION100
3.33-4.20.1761400.14233875X-RAY DIFFRACTION100
4.2-55.360.17221450.17223883X-RAY DIFFRACTION99.93

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