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- PDB-2c23: 14-3-3 Protein Beta (Human) in complex with exoenzyme S peptide -

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Basic information

Entry
Database: PDB / ID: 2c23
Title14-3-3 Protein Beta (Human) in complex with exoenzyme S peptide
Components
  • 14-3-3 BETA/ALPHA
  • EXOENZYME S PEPTIDE
KeywordsSIGNALING PROTEIN / 14-3-3 / YWHAB / EXOS / EXOENZYME S / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / ACETYLATION / ALTERNATIVE INITIATION / PHOSPHORYLATION / CELL REGULATOR PROTEIN
Function / homology
Function and homology information


negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling ...negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / Frs2-mediated activation / protein kinase inhibitor activity / positive regulation of catalytic activity / glycosyltransferase activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / nucleotidyltransferase activity / GTPase activator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Negative regulation of MAPK pathway / histone deacetylase binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / melanosome / Signaling by BRAF and RAF1 fusions / toxin activity / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / extracellular region / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein beta/alpha / Exoenzyme S
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
PSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsElkins, J.M. / Schoch, G.A. / Yang, X. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Doyle, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family.
Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M.
History
DepositionSep 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 BETA/ALPHA
P: EXOENZYME S PEPTIDE


Theoretical massNumber of molelcules
Total (without water)29,3532
Polymers29,3532
Non-polymers00
Water0
1
A: 14-3-3 BETA/ALPHA
P: EXOENZYME S PEPTIDE

A: 14-3-3 BETA/ALPHA
P: EXOENZYME S PEPTIDE


Theoretical massNumber of molelcules
Total (without water)58,7064
Polymers58,7064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4570 Å2
ΔGint-28.1 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.908, 86.841, 121.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE PROTEIN IS A DIMER IN SOLUTION, BUT SINCE IN THIS ENTRY IT IS IN COMPLEX WITH A PEPTIDE (CHAIN P), THE ENTRY IS MARKED AS TETRAMERIC

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Components

#1: Protein 14-3-3 BETA/ALPHA


Mass: 28236.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTVHR21-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31946
#2: Protein/peptide EXOENZYME S PEPTIDE


Mass: 1116.287 Da / Num. of mol.: 1 / Fragment: 14-3-3 BINDING REGION, RESIDUES 421-431 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: Q51451
Sequence detailsRESIDUES 240-245 ARE CLONING ARTEFACT FOR CHAIN A. THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF ...RESIDUES 240-245 ARE CLONING ARTEFACT FOR CHAIN A. THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPONDS TO GENBANK ENTRY BC001359.2 (HOMO SAPIENS TYROSINE 3-MONOOXYGENASE ACTIVATION PROTEIN BETA POLYPEPTIDE TRANSCRIPT VARIANT 2)

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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: 2.81 Å3/Da / Density % sol: 55.9 %
Crystal growpH: 8
Details: 0.05M MGCL2,0.1M HEPES PH7.5, 30% PEG MME 550, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99188
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 2.65→49.33 Å / Num. obs: 9558 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQ0

2bq0


Resolution: 2.65→60.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.677 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 538 5.6 %RANDOM
Rwork0.221 ---
obs0.224 8996 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--5.46 Å20 Å2
3----4.78 Å2
Refinement stepCycle: LAST / Resolution: 2.65→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 0 0 1839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221864
X-RAY DIFFRACTIONr_bond_other_d0.0020.021677
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9732519
X-RAY DIFFRACTIONr_angle_other_deg0.87433897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40825.56888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.932159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined0.2490.2480
X-RAY DIFFRACTIONr_nbd_other0.1750.21719
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2935
X-RAY DIFFRACTIONr_nbtor_other0.0890.21068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.90831300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.63651874
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.577761
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.61411645
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 42
Rwork0.339 650

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