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- PDB-6eih: The crystal structure of 14-3-3 epsilon in complex with the phosp... -

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Basic information

Entry
Database: PDB / ID: 6eih
TitleThe crystal structure of 14-3-3 epsilon in complex with the phosphorylated NELFE peptide
Components
  • 14-3-3 protein epsilon
  • SER-ILE-SEP-ARG
KeywordsPROTEIN BINDING / 14-3-3 / NELF
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 / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane ...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 / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cytoplasmic pattern recognition receptor signaling pathway / regulation of heart rate by cardiac conduction / calcium channel regulator activity / protein localization to nucleus / phosphoserine residue binding / Regulation of HSF1-mediated heat shock response / protein targeting / HSF1 activation / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 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 / regulation of mitotic cell cycle / regulation of cytosolic calcium ion concentration / substantia nigra development / AURKA Activation by TPX2 / protein sequestering activity / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / hippocampus development / mitochondrial membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / melanosome / MAPK cascade / cellular response to heat / MHC class II protein complex binding / 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 / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsAkutsu, M. / Wagner, S.A. / Beli, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
Emmy Noether Program5342/1-1 Germany
SFBSFB 1177 Germany
Marie Curie Career Integration Grant from the European Commission630763
LOEWE program Ubiquitin Networks Germany
CitationJournal: Nat Commun / Year: 2018
Title: p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage.
Authors: Borisova, M.E. / Voigt, A. / Tollenaere, M.A.X. / Sahu, S.K. / Juretschke, T. / Kreim, N. / Mailand, N. / Choudhary, C. / Bekker-Jensen, S. / Akutsu, M. / Wagner, S.A. / Beli, P.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly ...diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.oligomeric_count ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein epsilon
P: SER-ILE-SEP-ARG


Theoretical massNumber of molelcules
Total (without water)26,9142
Polymers26,9142
Non-polymers00
Water724
1
A: 14-3-3 protein epsilon
P: SER-ILE-SEP-ARG

A: 14-3-3 protein epsilon
P: SER-ILE-SEP-ARG


Theoretical massNumber of molelcules
Total (without water)53,8274
Polymers53,8274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3370 Å2
ΔGint-29 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.290, 81.186, 81.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26371.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: unidentified plasmid (others) / References: UniProt: P62258
#2: Protein/peptide SER-ILE-SEP-ARG


Mass: 542.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% pentaerythritol propoxylate, 0.2M sodium thiocyanate, 0.1M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→46 Å / Num. obs: 7463 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 18.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
MOLREPphasing
REFMAC5.8.0123refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.769 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 757 10.2 %RANDOM
Rwork0.1716 ---
obs0.1789 6692 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.54 Å2 / Biso mean: 50.554 Å2 / Biso min: 31.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--1.14 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 2.7→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 0 4 1859
Biso mean---40.78 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191882
X-RAY DIFFRACTIONr_bond_other_d0.0020.021807
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9822540
X-RAY DIFFRACTIONr_angle_other_deg0.95734158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6135232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17724.48387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74715348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2431513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022099
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 48 -
Rwork0.216 484 -
all-532 -
obs--100 %

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