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- PDB-3ubw: Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a sm... -

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Basic information

Entry
Database: PDB / ID: 3ubw
TitleComplex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen
Components
  • 14-3-3 protein epsilon
  • Myeloid leukemia factor 1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / Adapter protein / signaling protein / 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
(3S)-pyrrolidin-3-ol / 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: 1.9 Å
AuthorsMolzan, M. / Weyand, M. / Rose, R. / 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 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references

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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)32,2588
Polymers31,8002
Non-polymers4586
Water2,738152
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)64,51516
Polymers63,6004
Non-polymers91512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5340 Å2
ΔGint-17 kcal/mol
Surface area23810 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-2 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.030, 81.310, 81.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 30049.971 Da / Num. of mol.: 1 / Fragment: delta C, UNP residues 1-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62258
#2: Protein/peptide Myeloid leukemia factor 1 / Myelodysplasia-myeloid leukemia factor 1


Mass: 1749.922 Da / Num. of mol.: 1 / Fragment: phospho- 14-3-3 binding motif, UNP residues 29-42 / Source method: obtained synthetically / Details: Synthetic peptide / 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.: 5 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-6SP / (3S)-pyrrolidin-3-ol


Mass: 87.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: For crystallization of the 14-3-3 /MLF129-42 peptide complex, protein and peptide were mixed in a 1:1.5 molar ratio in 20 mM Hepes/NaOH pH 7.5, 2 mM MgCl2 and 2 mM 2-ME and set up for ...Details: For crystallization of the 14-3-3 /MLF129-42 peptide complex, protein and peptide were mixed in a 1:1.5 molar ratio in 20 mM Hepes/NaOH pH 7.5, 2 mM MgCl2 and 2 mM 2-ME and set up for crystallization in 0.1 M Na-Citrate pH 5.6 and 35% tert-butanol at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2008
RadiationMonochromator: Al1/Al1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.42 Å / Num. all: 20865 / Num. obs: 20904 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→2.2 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.67 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.42 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.365 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23838 1042 5 %RANDOM
Rwork0.18029 ---
all0.18322 20865 --
obs0.18322 19794 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 31 152 2077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222072
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2041.9922818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.325.075266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67524.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115.039385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4821516
X-RAY DIFFRACTIONr_chiral_restr0.2360.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211563
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_it1.3911.51275
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45722047
X-RAY DIFFRACTIONr_scbond_it4.0323797
X-RAY DIFFRACTIONr_scangle_it6.5284.5764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 77 -
Rwork0.24 1463 -
obs--100 %

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