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- PDB-7oqs: Ternary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ177 -

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Basic information

Entry
Database: PDB / ID: 7oqs
TitleTernary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ177
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 / blood vessel endothelial cell migration / Regulation of CDH11 function / positive regulation of embryonic development / 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 / blood vessel endothelial cell migration / Regulation of CDH11 function / positive regulation of embryonic development / 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 / positive regulation of blood vessel endothelial cell migration / positive regulation of cell size / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / bicellular tight junction / negative regulation of keratinocyte proliferation / 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 protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / stress fiber / positive regulation of stress fiber assembly / positive regulation of protein localization / ruffle / positive regulation of cell adhesion / 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 / negative regulation of angiogenesis / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / chemotaxis / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / signaling receptor activity / lamellipodium / 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 / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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-0BS / 14-3-3 protein sigma / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 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
P: Amot-p130 phosphopeptide (pS175)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2714
Polymers29,8532
Non-polymers4182
Water4,630257
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)60,5428
Polymers59,7074
Non-polymers8364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4510 Å2
ΔGint-28 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.425, 111.590, 62.467
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

21A-646-

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-0BS / 2-(1,3-benzodioxol-5-yl)-~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]ethanamide


Mass: 393.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
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: 1.34→62.47 Å / Num. obs: 64885 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.28 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.044 / Net I/σ(I): 13
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3190 / CC1/2: 0.752 / Rpim(I) all: 0.947 / % 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: 1.34→55.79 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6326 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1952 3354 5.17 %
Rwork0.1783 61497 -
obs0.1791 64851 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.34→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 29 257 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871946
X-RAY DIFFRACTIONf_angle_d0.972633
X-RAY DIFFRACTIONf_chiral_restr0.06289
X-RAY DIFFRACTIONf_plane_restr0.0057343
X-RAY DIFFRACTIONf_dihedral_angle_d18.2175739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.33421610.28052543X-RAY DIFFRACTION99.96
1.36-1.380.26881520.26262489X-RAY DIFFRACTION99.96
1.38-1.40.28331380.25312540X-RAY DIFFRACTION100
1.4-1.420.29161430.24762517X-RAY DIFFRACTION100
1.42-1.450.26181350.22992568X-RAY DIFFRACTION99.96
1.45-1.470.22871110.2162552X-RAY DIFFRACTION99.96
1.47-1.50.22261240.20592551X-RAY DIFFRACTION100
1.5-1.530.22281220.20592548X-RAY DIFFRACTION99.89
1.53-1.570.21251180.19882555X-RAY DIFFRACTION100
1.57-1.60.2491360.19612545X-RAY DIFFRACTION100
1.6-1.640.20741490.19532564X-RAY DIFFRACTION100
1.64-1.690.19981440.18562523X-RAY DIFFRACTION100
1.69-1.740.18971390.18872559X-RAY DIFFRACTION100
1.74-1.790.23231620.19292528X-RAY DIFFRACTION100
1.79-1.860.21431290.19042544X-RAY DIFFRACTION100
1.86-1.930.20081560.17952550X-RAY DIFFRACTION100
1.93-2.020.19941260.17562563X-RAY DIFFRACTION99.96
2.02-2.130.17851410.16532561X-RAY DIFFRACTION99.96
2.13-2.260.17981430.15882573X-RAY DIFFRACTION100
2.26-2.430.15591530.15452559X-RAY DIFFRACTION100
2.43-2.680.16951280.15972613X-RAY DIFFRACTION100
2.68-3.070.16991360.16472592X-RAY DIFFRACTION100
3.07-3.860.18151480.16132638X-RAY DIFFRACTION100
3.86-55.790.19351600.17492722X-RAY DIFFRACTION100

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