- PDB-3ubw: Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a sm... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ubw
Title
Complex 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
Keywords
SIGNALING 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
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
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal grow
Temperature: 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
Resolution: 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
Name
Version
Classification
XDS
datascaling
PHASER
phasing
REFMAC
5.5.0109
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23838
1042
5 %
RANDOM
Rwork
0.18029
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all
0.18322
20865
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obs
0.18322
19794
100 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 31.014 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.64 Å2
0 Å2
0 Å2
2-
-
-0.53 Å2
0 Å2
3-
-
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1.17 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→46.42 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1894
0
31
152
2077
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.026
0.022
2072
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.204
1.992
2818
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
14.32
5.075
266
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.675
24.4
100
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.831
15.039
385
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.482
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.236
0.2
313
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
1563
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.391
1.5
1275
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.457
2
2047
X-RAY DIFFRACTION
r_scbond_it
4.032
3
797
X-RAY DIFFRACTION
r_scangle_it
6.528
4.5
764
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.276
77
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Rwork
0.24
1463
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obs
-
-
100 %
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