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

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Basic information

Entry
Database: PDB / ID: 7nmx
TitleCrystal structure of 14-3-3 sigma in complex with 13mer Amot-p130 peptide and fragment 12
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-K7Q / 14-3-3 protein sigma / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 23, 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

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)30,3579
Polymers29,8532
Non-polymers5037
Water4,143230
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)60,71318
Polymers59,7074
Non-polymers1,00614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5090 Å2
ΔGint-76 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.469, 111.993, 62.699
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-304-

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 , 5 types, 237 molecules

#3: Chemical ChemComp-K7Q / ~{N}-(2-azanylethyl)-2-carbamimidoyl-7-methoxy-1-benzothiophene-4-carboxamide


Mass: 292.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.44 %
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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.3→33.15 Å / Num. obs: 12756 / % possible obs: 97.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 8.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 12.5 / Num. unique obs: 925 / CC1/2: 0.993

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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: 2.3→29.89 Å / SU ML: 0.213 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.6736 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2265 652 5.11 %
Rwork0.1713 12100 -
obs0.174 12752 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 26 230 2092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261916
X-RAY DIFFRACTIONf_angle_d0.50652587
X-RAY DIFFRACTIONf_chiral_restr0.0315287
X-RAY DIFFRACTIONf_plane_restr0.0024333
X-RAY DIFFRACTIONf_dihedral_angle_d14.31721181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.24291310.16762417X-RAY DIFFRACTION98.3
2.48-2.730.25611290.17422406X-RAY DIFFRACTION97.73
2.73-3.120.25341350.17832425X-RAY DIFFRACTION97.26
3.12-3.930.18551270.15782391X-RAY DIFFRACTION95.56
3.93-29.890.22371300.17992461X-RAY DIFFRACTION94.15

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