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- PDB-7nne: Crystal structure of 14-3-3 sigma in complex with 13mer Amot-p130... -

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Basic information

Entry
Database: PDB / ID: 7nne
TitleCrystal structure of 14-3-3 sigma in complex with 13mer Amot-p130 peptide and fragment 22
Components
  • 14-3-3 protein sigma
  • Amot-p130 phosphopeptide (pS175)
KeywordsSIGNALING PROTEIN / protein-peptide complex fragment soaking
Function / homology
Function and homology information


establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / Regulation of CDH11 function / positive regulation of embryonic development / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / negative regulation of vascular permeability / gastrulation with mouth forming second ...establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / Regulation of CDH11 function / positive regulation of embryonic development / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / negative regulation of vascular permeability / gastrulation with mouth forming second / Signaling by Hippo / cell-cell junction assembly / 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 / Regulation of localization of FOXO transcription factors / endocytic vesicle / keratinocyte proliferation / positive regulation of cell size / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / bicellular tight junction / positive regulation of blood vessel endothelial cell migration / establishment of skin barrier / vasculogenesis / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / stress fiber / positive regulation of protein localization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of innate immune response / ruffle / protein sequestering activity / protein kinase A signaling / protein export from nucleus / regulation of cell migration / positive regulation of cell adhesion / negative regulation of angiogenesis / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / protein localization / cell junction / lamellipodium / regulation of protein localization / signaling receptor activity / actin cytoskeleton organization / cytoplasmic vesicle / positive regulation of cell growth / angiogenesis / in utero embryonic development / regulation of cell cycle / cadherin binding / external side of plasma membrane / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / 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-K92 / 14-3-3 protein sigma / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)30,2004
Polymers29,8532
Non-polymers3472
Water5,531307
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)60,4008
Polymers59,7074
Non-polymers6944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5420 Å2
ΔGint-59 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.277, 111.256, 62.438
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-417-

HOH

21A-685-

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-K92 / 5-[3-(2-azanylethyl)imidazol-4-yl]-4-phenyl-thiophene-2-carboximidamide


Mass: 311.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5S / 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.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 48.93 %
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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.96→62.47 Å / Num. obs: 20993 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 19.51 Å2 / CC1/2: 0.986 / Rpim(I) all: 0.146 / Net I/σ(I): 4.6
Reflection shellResolution: 1.96→2.01 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1506 / CC1/2: 0.477 / Rpim(I) all: 0.448

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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: 1.96→45.41 Å / SU ML: 0.2393 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 24.9611 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2601 1052 5.02 %
Rwork0.2109 19892 -
obs0.2133 20944 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.75 Å2
Refinement stepCycle: LAST / Resolution: 1.96→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 23 307 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221959
X-RAY DIFFRACTIONf_angle_d0.48022637
X-RAY DIFFRACTIONf_chiral_restr0.0313291
X-RAY DIFFRACTIONf_plane_restr0.0023340
X-RAY DIFFRACTIONf_dihedral_angle_d16.4841203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.050.31181440.27372388X-RAY DIFFRACTION98.52
2.05-2.160.32641290.25682470X-RAY DIFFRACTION99.65
2.16-2.290.28791340.23932450X-RAY DIFFRACTION99.73
2.29-2.470.27941210.22272471X-RAY DIFFRACTION100
2.47-2.720.23871460.22152459X-RAY DIFFRACTION100
2.72-3.110.26821360.20412499X-RAY DIFFRACTION100
3.11-3.920.21711290.17992510X-RAY DIFFRACTION100
3.92-45.410.24841130.19332645X-RAY DIFFRACTION99.93

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