SAXSdb — 7c8e

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1. Protein Identity and Related Structures Protein Identity & Related Structures

14-3-3 protein epsilon

Homo sapiens

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 1–232 Chain B； UniProt 1–232	Not recorded	9J10 × 2 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

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 7C8E	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 oligomeric state 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
3UBW Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen Deposited 2011-10-25	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 1–234（234 aa） Fragment：delta C, UNP residues 1-234	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
3UBW Complex of 14-3-3 isoform epsilon, a Mlf1 phosphopeptide and a small fragment hit from a FBDD screen Deposited 2011-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–234（234 aa） Fragment：delta C, UNP residues 1-234	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
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
8DGM 14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide Deposited 2022-06-24	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 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 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 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 12 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 35–266； UniProt 1–232 Author chain B； PDBConstruct 35–266； UniProt 1–232

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7c8e
Deposition date deposition_date	2020-05-30
Structure title title	Crystal Structure of 14-3-3 epsilon with 9J10 peptide
Keywords keywords	Signaling protein, Phosphopeptide binding, peptide complex, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.06 Å
Radius of gyration Rg (electron density) rg_electron	26.24 Å
Forward intensity I(0) i0	48251200.00
Molecular weight molecular_weight	52742.0 kDa
Excluded volume excluded_volume	65460 Å³
Envelope volume envelope_volume	84632 Å³
Hydration-shell volume shell_volume	26979 Å³
Envelope diameter envelope_diameter	86.2 Å
Shell Rg shell_rg	33.51 Å
Envelope Rg envelope_rg	25.75 Å
Shape Rg shape_rg	26.25 Å
Total Rg total_rg	26.99 Å
Total atoms total_atoms	3700
Residues n_residues	471
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.8 Å
Rg (real space) rg_real	27.00 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.8250e+07
I(0) uncertainty (real space) i0_real_error	6.5210e+05
Rg (reciprocal space) rg_reciprocal	27.02 Å
I(0) (reciprocal space) i0_reciprocal	48250000.0000
Solution quality estimate total_estimate	0.9158
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.635
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7369000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.985; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	14-3-3 protein epsilon
Molecular weight formula_weight	30170.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3735

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	9J10
Molecular weight formula_weight	1524.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

LNRTPGRRRNSN

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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8. Citations (1)

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Unit-cell length a length_a	59.470 Å
Unit-cell length b length_b	83.350 Å
Unit-cell length c length_c	118.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.160 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2242
R_work r_work	0.2217
R_free r_free	0.2705

fit	/app/data/saxs_computation/c8/7c8e/7c8e.fit
pddf	/app/data/pr_computation/c8/7c8e/7c8e.pr.out
profile	/app/data/saxs_computation/c8/7c8e/7c8e.dat

Crystal Structure of 14-3-3 epsilon with 9J10 peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

14-3-3 protein epsilon

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)