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- PDB-7oqu: Ternary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ180 -

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Basic information

Entry
Database: PDB / ID: 7oqu
TitleTernary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ180
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 / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability ...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 / 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 / positive regulation of cell size / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / bicellular tight junction / 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 / vasculogenesis / negative regulation of stem cell proliferation / stress fiber / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of stress fiber assembly / ruffle / positive regulation of cell adhesion / protein sequestering activity / 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 / negative regulation of angiogenesis / regulation of cell migration / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / actin filament / intrinsic apoptotic signaling pathway in response to DNA damage / chemotaxis / intracellular 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 / 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-0BL / 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 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 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)30,3296
Polymers29,8532
Non-polymers4764
Water4,216234
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)60,65812
Polymers59,7074
Non-polymers9518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4630 Å2
ΔGint-59 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.611, 111.835, 62.277
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-303-

MG

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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 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

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Non-polymers , 4 types, 238 molecules

#3: Chemical ChemComp-0BL / (2~{S},3~{S})-~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-3-methyl-2,3-dihydro-1-benzofuran-2-carboxamide


Mass: 391.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N3O2S / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.095 M Hepes pH7.5, 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→66.45 Å / Num. obs: 57063 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13 % / Rmerge(I) obs: 1.672 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2810 / CC1/2: 0.799 / % 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→66.45 Å / SU ML: 0.1291 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.9852 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1824 3876 3.53 %
Rwork0.1714 105917 -
obs0.1718 57039 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.92 Å2
Refinement stepCycle: LAST / Resolution: 1.4→66.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 31 234 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851908
X-RAY DIFFRACTIONf_angle_d0.93272579
X-RAY DIFFRACTIONf_chiral_restr0.0613284
X-RAY DIFFRACTIONf_plane_restr0.0056335
X-RAY DIFFRACTIONf_dihedral_angle_d16.1136720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.26661400.28753823X-RAY DIFFRACTION99.92
1.42-1.440.28221370.27313744X-RAY DIFFRACTION99.92
1.44-1.450.2261410.25123804X-RAY DIFFRACTION99.87
1.45-1.470.27261330.23413730X-RAY DIFFRACTION99.97
1.47-1.490.23461370.21733788X-RAY DIFFRACTION99.9
1.49-1.520.23071390.21943775X-RAY DIFFRACTION99.97
1.52-1.540.21711410.21583785X-RAY DIFFRACTION99.95
1.54-1.570.22321400.20853786X-RAY DIFFRACTION99.97
1.57-1.590.21891370.20713767X-RAY DIFFRACTION99.87
1.59-1.620.22741430.20563824X-RAY DIFFRACTION100
1.62-1.650.20371370.19773737X-RAY DIFFRACTION99.95
1.65-1.690.17431350.18613806X-RAY DIFFRACTION100
1.69-1.720.25561390.18983799X-RAY DIFFRACTION99.97
1.72-1.760.23081360.18483795X-RAY DIFFRACTION100
1.76-1.810.19031370.18053738X-RAY DIFFRACTION100
1.81-1.860.18031390.17543799X-RAY DIFFRACTION100
1.86-1.910.18251390.17673777X-RAY DIFFRACTION100
1.91-1.970.22241360.1663789X-RAY DIFFRACTION100
1.97-2.040.16581410.16943787X-RAY DIFFRACTION100
2.04-2.130.1551390.15533767X-RAY DIFFRACTION100
2.13-2.220.18121360.1543824X-RAY DIFFRACTION99.95
2.22-2.340.21891330.14863768X-RAY DIFFRACTION100
2.34-2.490.13141380.13143779X-RAY DIFFRACTION100
2.49-2.680.1921390.15793808X-RAY DIFFRACTION100
2.68-2.950.18771400.16413762X-RAY DIFFRACTION100
3.37-4.250.16511400.14683798X-RAY DIFFRACTION100

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