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3ubw

Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen

Method: X-RAY DIFFRACTION Dmax: 65.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

14-3-3 protein epsilon

Homo sapiens

UniProt P62258

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–234 Fragment：delta C, UNP residues 1-234 Non-standard monomer：Yes (specific site not provided by mmCIF) Myeloid leukemia factor 1 × 2 （P58340） TBU TERTIARY-BUTYL ALCOHOL × 10 6SP (3S)-pyrrolidin-3-ol × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；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 1.90 Å R-free 0.238
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–234 Fragment：delta C, UNP residues 1-234 Non-standard monomer：Yes (specific site not provided by mmCIF) Myeloid leukemia factor 1 × 1 （P58340） TBU TERTIARY-BUTYL ALCOHOL × 5 6SP (3S)-pyrrolidin-3-ol × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；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 1.90 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3UBW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BR9 14-3-3 Protein Epsilon (Human) Complexed to Peptide Deposited 2005-05-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；40% MPD, 5% PEG10000, 0.1M CACODYLATE PH6.5. PROTEIN IN 150MM NACL, 50MM TRIS PH8, pH 8.00
Resolution 1.75 Å R-free 0.239
3UAL Crystal Structure of 14-3-3 epsilon with Mlf1 peptide Deposited 2011-10-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–232（232 aa） Fragment：UNP residues 1-232
Not recorded TBU TERTIARY-BUTYL ALCOHOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.222
3UAL Crystal Structure of 14-3-3 epsilon with Mlf1 peptide Deposited 2011-10-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–232（232 aa） Fragment：UNP residues 1-232
Not recorded TBU TERTIARY-BUTYL ALCOHOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.222
6EIH The crystal structure of 14-3-3 epsilon in complex with the phosphorylated NELFE peptide Deposited 2017-09-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 3–232（230 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；40% pentaerythritol propoxylate, 0.2M sodium thiocyanate, 0.1M HEPES, pH 7.0
Resolution 2.70 Å R-free 0.241
7C8E Crystal Structure of 14-3-3 epsilon with 9J10 peptide Deposited 2020-05-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–232（232 aa）
Chain B 1–232（232 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；28% PEG 400, 0.1M Hepes pH 7.5, 0.2M Calcium chloride
Resolution 3.16 Å R-free 0.271
8DGM 14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide Deposited 2022-06-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–255（255 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.8 M ammonium sulfate, 0.1 M HEPES pH 7.5, 5% (v/v) MPD
Resolution 3.20 Å R-free 0.266
8DGN 14-3-3 epsilon bound to phosphorylated PEAK2 (pS826) peptide Deposited 2022-06-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–255（255 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.8 M ammonium sulfate, 0.1 M HEPES pH 7.5, 5% (v/v) MPD
Resolution 3.16 Å R-free 0.295
8DGP 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide Deposited 2022-06-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–255（255 aa）
Chain B 1–255（255 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.35；293 K；2M ammonium sulfate, 0.1 M sodium bicine pH 9.35, 5% (v/v) 2-methyl-2,4,-pentandiol (MPD)
Resolution 2.70 Å R-free 0.233
8DGP 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) peptide Deposited 2022-06-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–255（255 aa）
Chain D 1–255（255 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.35；293 K；2M ammonium sulfate, 0.1 M sodium bicine pH 9.35, 5% (v/v) 2-methyl-2,4,-pentandiol (MPD)
Resolution 2.70 Å R-free 0.233
8DP5 Structure of the PEAK3/14-3-3 complex Deposited 2022-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–255（255 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；A final concentration of 0.1% of Octyl-beta-Glucoside (C14H28O6) was added to the sample before freezing.
cryo-EM vitrification conditions Cryogen ETHANE；blot time = 7s blot force = 4
Resolution 3.10 Å
8Q1S Pathogenic mutations of human phosphorylation sites affect protein-protein interactions Deposited 2023-08-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–255（255 aa）
Chain B 1–255（255 aa）
Not recorded BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；19% PEG 3350, 0.35 M NaBr, 0.1 M BisTris-Propane pH 6.5
Resolution 3.23 Å R-free 0.279

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433E_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 28–261； UniProt 1–234

Myeloid leukemia factor 1

OrganismNot specified

UniProt P58340

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain P； UniProt 29–42 Fragment：phospho- 14-3-3 binding motif, UNP residues 29-42 Non-standard monomer：Yes (specific site not provided by mmCIF) 14-3-3 protein epsilon × 2 （P62258） TBU TERTIARY-BUTYL ALCOHOL × 10 6SP (3S)-pyrrolidin-3-ol × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；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 1.90 Å R-free 0.238
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain P； UniProt 29–42 Fragment：phospho- 14-3-3 binding motif, UNP residues 29-42 Non-standard monomer：Yes (specific site not provided by mmCIF) 14-3-3 protein epsilon × 1 （P62258） TBU TERTIARY-BUTYL ALCOHOL × 5 6SP (3S)-pyrrolidin-3-ol × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；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 1.90 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3UBW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3UAL Crystal Structure of 14-3-3 epsilon with Mlf1 peptide Deposited 2011-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 29–42（14 aa） Fragment：UNP residues 29-42
Non-standard monomer：Yes (specific site not provided by mmCIF) TBU TERTIARY-BUTYL ALCOHOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.222
3UAL Crystal Structure of 14-3-3 epsilon with Mlf1 peptide Deposited 2011-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 29–42（14 aa） Fragment：UNP residues 29-42
Non-standard monomer：Yes (specific site not provided by mmCIF) TBU TERTIARY-BUTYL ALCOHOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M Na-Citrate, 35% tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.222

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MLF1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain P； PDBConstruct 1–14； UniProt 29–42

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3ubw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ubw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ubw
Deposition date deposition_date2011-10-25
Structure title titleComplex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen
Keywords keywordsAdapter protein, signaling protein, SIGNALING PROTEIN-PROTEIN BINDING complex; SIGNALING PROTEIN/PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.83 Å
Radius of gyration Rg (electron density) rg_electron18.75 Å
Forward intensity I(0) i013331500.00
Molecular weight molecular_weight27450.0 kDa
Excluded volume excluded_volume34481 ų
Envelope volume envelope_volume40340 ų
Hydration-shell volume shell_volume18230 ų
Envelope diameter envelope_diameter67.2 Å
Shell Rg shell_rg25.03 Å
Envelope Rg envelope_rg19.30 Å
Shape Rg shape_rg18.71 Å
Total Rg total_rg19.82 Å
Total atoms total_atoms1925
Residues n_residues235
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.0 Å
Rg (real space) rg_real19.80 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real1.3330e+07
I(0) uncertainty (real space) i0_real_error1.7170e+05
Rg (reciprocal space) rg_reciprocal19.81 Å
I(0) (reciprocal space) i0_reciprocal13330000.0000
Solution quality estimate total_estimate0.8124
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7 Å
Skewness Skewness skewness0.323
Kurtosis Kurtosis kurtosis-0.230
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2690000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3ubwA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain
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8. Citations (1)

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9. Files and Curves (10)