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- PDB-7np2: Crystal structure of 14-3-3 sigma in complex with 20mer Amot-p130... -

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Basic information

Entry
Database: PDB / ID: 7np2
TitleCrystal structure of 14-3-3 sigma in complex with 20mer Amot-p130 peptide
Components
  • 14-3-3 protein sigma
  • Amot-p130 phosphopeptide (pS175)
KeywordsSIGNALING PROTEIN / protein-peptide complex
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 / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / chemotaxis / 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
14-3-3 protein sigma / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsCentorrino, F. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Fragment-based exploration of the 14-3-3/Amot-p130 interface.
Authors: Centorrino, F. / Andlovic, B. / Cossar, P. / Brunsveld, L. / Ottmann, C.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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)30,5294
Polymers30,4692
Non-polymers602
Water6,846380
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)61,0588
Polymers60,9384
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5040 Å2
ΔGint-58 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.419, 111.941, 62.673
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-414-

HOH

21A-753-

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: 2242.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.15 %
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: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.27→41.21 Å / Num. obs: 76770 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 12.04 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.098 / Net I/σ(I): 8.8
Reflection shellResolution: 1.27→1.3 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 76770 / CC1/2: 0.827 / Rpim(I) all: 0.463

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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: 1.27→41.21 Å / SU ML: 0.0829 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.5562 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1815 3905 5.1 %
Rwork0.1661 72666 -
obs0.1669 76571 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.99 Å2
Refinement stepCycle: LAST / Resolution: 1.27→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 2 380 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771994
X-RAY DIFFRACTIONf_angle_d0.87852700
X-RAY DIFFRACTIONf_chiral_restr0.0575301
X-RAY DIFFRACTIONf_plane_restr0.006353
X-RAY DIFFRACTIONf_dihedral_angle_d19.3003775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.2221280.21782524X-RAY DIFFRACTION97.86
1.28-1.30.21851360.20212578X-RAY DIFFRACTION99.96
1.3-1.320.2021350.19452568X-RAY DIFFRACTION100
1.32-1.340.18591350.19132613X-RAY DIFFRACTION100
1.34-1.360.1931540.19222514X-RAY DIFFRACTION100
1.36-1.380.22331480.19742562X-RAY DIFFRACTION100
1.38-1.40.18391190.19342611X-RAY DIFFRACTION100
1.4-1.420.18681430.18872570X-RAY DIFFRACTION100
1.42-1.440.23791250.18392570X-RAY DIFFRACTION100
1.44-1.470.20421360.18012556X-RAY DIFFRACTION100
1.47-1.50.19721580.17052564X-RAY DIFFRACTION99.96
1.5-1.530.18041420.17022601X-RAY DIFFRACTION100
1.53-1.560.17511320.16852566X-RAY DIFFRACTION99.96
1.56-1.60.18141430.16582565X-RAY DIFFRACTION100
1.6-1.640.18321370.16272585X-RAY DIFFRACTION100
1.64-1.680.17731450.1632589X-RAY DIFFRACTION100
1.68-1.730.19171370.16082612X-RAY DIFFRACTION100
1.73-1.790.20191340.17172598X-RAY DIFFRACTION100
1.79-1.850.16991500.16792556X-RAY DIFFRACTION100
1.85-1.930.17911530.16632591X-RAY DIFFRACTION100
1.93-2.010.18321320.15932605X-RAY DIFFRACTION100
2.01-2.120.16181420.15192612X-RAY DIFFRACTION100
2.12-2.250.17161420.14922603X-RAY DIFFRACTION100
2.25-2.430.17621380.14662627X-RAY DIFFRACTION100
2.43-2.670.17121380.15732648X-RAY DIFFRACTION100
2.67-3.060.17951400.1662629X-RAY DIFFRACTION100
3.06-3.850.1741370.15462670X-RAY DIFFRACTION100
3.85-41.210.18351460.17872779X-RAY DIFFRACTION100

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