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- PDB-3ual: Crystal Structure of 14-3-3 epsilon with Mlf1 peptide -

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Basic information

Entry
Database: PDB / ID: 3ual
TitleCrystal Structure of 14-3-3 epsilon with Mlf1 peptide
Components
  • 14-3-3 protein epsilon
  • Myeloid leukemia factor 1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / Adapter protein / ALL HELICAL / PHOSPHOPETIDE / SIGNALING PROTEIN-PROTEIN BINDING 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 / regulation of cell cycle G1/S phase transition / NADE modulates death signalling ...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 / regulation of cell cycle G1/S phase transition / NADE modulates death signalling / myeloid progenitor cell differentiation / 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 / ciliary basal body / regulation of signal transduction by p53 class mediator / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial membrane / hippocampus development / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / cerebral cortex development / cilium / 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 / cell cycle / protein heterodimerization activity / protein domain specific binding / focal adhesion / DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / signal transduction / DNA binding / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Myeloid leukemia factor / Myelodysplasia-myeloid leukemia factor 1-interacting 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 ...Myeloid leukemia factor / Myelodysplasia-myeloid leukemia factor 1-interacting 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
TERTIARY-BUTYL ALCOHOL / Myeloid leukemia factor 1 / 14-3-3 protein epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeyand, M. / Ottmann, C.
CitationJournal: Febs J. / Year: 2012
Title: Structural insights of the MLF1/14-3-3 interaction.
Authors: Molzan, M. / Weyand, M. / Rose, R. / Ottmann, C.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Myeloid leukemia factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5905
Polymers28,3672
Non-polymers2223
Water2,864159
1
A: 14-3-3 protein epsilon
P: Myeloid leukemia factor 1
hetero molecules

A: 14-3-3 protein epsilon
P: Myeloid leukemia factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17910
Polymers56,7354
Non-polymers4456
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5070 Å2
ΔGint-20 kcal/mol
Surface area23840 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-4 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.980, 81.460, 82.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-291-

HOH

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Components

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


Mass: 26617.340 Da / Num. of mol.: 1 / Fragment: UNP residues 1-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli (E. coli) / References: UniProt: P62258
#2: Protein/peptide Myeloid leukemia factor 1 / Myelodysplasia-myeloid leukemia factor 1


Mass: 1749.922 Da / Num. of mol.: 1 / Fragment: UNP residues 29-42 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P58340
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97906 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2008
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 24815 / Num. obs: 24289 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.061 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3568 / Rsym value: 0.45 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR9

2br9


Resolution: 1.8→35.27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.996 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1215 5 %RANDOM
Rwork0.1719 ---
all0.17442 24508 --
obs0.17442 23072 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 15 159 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9882801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32924.423104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05115.038395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5831517
X-RAY DIFFRACTIONr_chiral_restr0.1410.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.51251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00322017
X-RAY DIFFRACTIONr_scbond_it3.483808
X-RAY DIFFRACTIONr_scangle_it5.4844.5770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 88 -
Rwork0.21 1671 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -18.8512 Å / Origin y: 5.6095 Å / Origin z: 20.9416 Å
111213212223313233
T0.0446 Å20.0275 Å20.0005 Å2-0.0213 Å2-0.012 Å2--0.0728 Å2
L2.201 °20.5629 °20.3282 °2-1.2322 °20.2857 °2--1.4513 °2
S-0.0666 Å °-0.022 Å °0.0977 Å °0.0416 Å °-0.0204 Å °0.1128 Å °-0.0324 Å °-0.0162 Å °0.087 Å °

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