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- PDB-7c8e: Crystal Structure of 14-3-3 epsilon with 9J10 peptide -

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Basic information

Entry
Database: PDB / ID: 7c8e
TitleCrystal Structure of 14-3-3 epsilon with 9J10 peptide
Components
  • 14-3-3 protein epsilon
  • 9J10
KeywordsPROTEIN BINDING / Signaling protein / Phosphopeptide binding / peptide complex
Function / homology
Function and homology information


negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs ...negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / membrane repolarization during cardiac muscle cell action potential / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane / cytoplasmic pattern recognition receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of heart rate by cardiac conduction / protein localization to nucleus / calcium channel regulator activity / phosphoserine residue binding / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signaling adaptor activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / regulation of mitotic cell cycle / regulation of cytosolic calcium ion concentration / substantia nigra development / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial membrane / hippocampus development / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / melanosome / MHC class II protein complex binding / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
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 epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsMathivanan, S. / Sudhakar, S. / Bairy, S. / Kamariah, N. / Venkitaraman, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Cell Chem Biol / Year: 2021
Title: Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library.
Authors: Emery, A. / Hardwick, B.S. / Crooks, A.T. / Milech, N. / Watt, P.M. / Mithra, C. / Kumar, V. / Giridharan, S. / Sadasivam, G. / Mathivanan, S. / Sudhakar, S. / Bairy, S. / Bharatham, K. / ...Authors: Emery, A. / Hardwick, B.S. / Crooks, A.T. / Milech, N. / Watt, P.M. / Mithra, C. / Kumar, V. / Giridharan, S. / Sadasivam, G. / Mathivanan, S. / Sudhakar, S. / Bairy, S. / Bharatham, K. / Hurakadli, M.A. / Prasad, T.K. / Kamariah, N. / Muellner, M. / Coelho, M. / Torrance, C.J. / McKenzie, G.J. / Venkitaraman, A.R.
History
DepositionMay 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: 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 1.2Dec 8, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: 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 epsilon
B: 14-3-3 protein epsilon
C: 9J10
D: 9J10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5125
Polymers63,3904
Non-polymers1221
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, HOMO DIMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-14 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.470, 83.350, 118.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein epsilon / 14-3-3E


Mass: 30170.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62258
#2: Protein/peptide 9J10


Mass: 1524.584 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 400, 0.1M Hepes pH 7.5, 0.2M Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 3.16→68.234 Å / Num. obs: 10688 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC1/2: 0.995 / Rpim(I) all: 0.075 / Rrim(I) all: 0.163 / Rsym value: 0.145 / Net I/σ(I): 8.6
Reflection shellResolution: 3.16→3.33 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1516 / CC1/2: 0.698 / Rpim(I) all: 0.335 / Rrim(I) all: 0.729 / Rsym value: 0.645 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BR9

2br9


Resolution: 3.16→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / SU B: 26.123 / SU ML: 0.434 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 522 4.9 %RANDOM
Rwork0.2217 ---
obs0.2242 10115 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.04 Å2 / Biso mean: 62.732 Å2 / Biso min: 23.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2---0.72 Å20 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 3.16→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 8 29 3729
Biso mean--78.55 39.62 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133759
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173463
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.6435088
X-RAY DIFFRACTIONr_angle_other_deg1.1141.587974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50421.962209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30415648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8891531
X-RAY DIFFRACTIONr_chiral_restr0.0430.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
LS refinement shellResolution: 3.16→3.236 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.364 33 -
Rwork0.307 724 -
obs--98.83 %

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