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- PDB-7obd: Crystal structure of 14-3-3 sigma in complex with Phosphorylated ... -

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Basic information

Entry
Database: PDB / ID: 7obd
TitleCrystal structure of 14-3-3 sigma in complex with Phosphorylated and Farnesylated Rnd3 peptide and stabilizer Fusicoccin-A
Components
  • 14-3-3 protein sigma
  • Rho-related GTP-binding protein RhoE
KeywordsSIGNALING PROTEIN / 14-3-3 sigma protein-peptide-stabilizer complex
Function / homology
Function and homology information


RND3 GTPase cycle / 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 ...RND3 GTPase cycle / 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 / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / 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 / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / actin filament organization / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / actin cytoskeleton organization / cell adhesion / regulation of cell cycle / cadherin binding / Golgi membrane / focal adhesion / GTPase activity / protein kinase binding / GTP binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho-related GTP-binding protein RhoE / Small GTPase Rho / Small GTPase Rho domain profile. / 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 ...Rho-related GTP-binding protein RhoE / Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FARNESYL / FUSICOCCIN / 14-3-3 protein sigma / Rho-related GTP-binding protein RhoE
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCentorrino, F. / Andlovic, B. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: Cell Chem Biol / Year: 2023
Title: IFN alpha primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization.
Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, ...Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, F. / Kaiser, M. / Eickhoff, J. / Ottmann, C.
History
DepositionApr 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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
B: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5467
Polymers29,5752
Non-polymers9715
Water5,783321
1
A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules

A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,09214
Polymers59,1504
Non-polymers1,94310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7360 Å2
ΔGint-61 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.480, 111.339, 62.969
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-710-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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 Rho-related GTP-binding protein RhoE / Protein MemB / Rho family GTPase 3 / Rho-related GTP-binding protein Rho8 / Rnd3


Mass: 1348.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61587

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Non-polymers , 5 types, 326 molecules

#3: Chemical ChemComp-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.7, 24%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: Sep 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2→33.85 Å / Num. obs: 19555 / % possible obs: 98.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 9.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.04 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 953 / CC1/2: 0.937 / % possible all: 95.3

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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→33.84 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6216 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2104 977 5 %
Rwork0.1658 18569 -
obs0.168 19546 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.49 Å2
Refinement stepCycle: LAST / Resolution: 2→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 57 321 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211970
X-RAY DIFFRACTIONf_angle_d0.54652666
X-RAY DIFFRACTIONf_chiral_restr0.0326300
X-RAY DIFFRACTIONf_plane_restr0.002341
X-RAY DIFFRACTIONf_dihedral_angle_d15.38911191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.23811350.16952566X-RAY DIFFRACTION96.33
2.11-2.240.2211360.16522592X-RAY DIFFRACTION97.22
2.24-2.410.22481360.16952596X-RAY DIFFRACTION97.75
2.41-2.660.23131390.16712634X-RAY DIFFRACTION98.37
2.66-3.040.2031400.16882663X-RAY DIFFRACTION98.91
3.04-3.830.18641420.14942693X-RAY DIFFRACTION99.51
3.83-33.840.20271490.17582825X-RAY DIFFRACTION99.73

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