SAXSdb — 8dgn

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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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–255	Not recorded	Phosphorylated PEAK2 (pS826) peptide × 1	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

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 8DGN	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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 ligand/ion 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
8DGP 14-3-3 epsilon bound to phosphorylated PEAK3 (pS69) 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 × 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 4–258； UniProt 1–255

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	8dgn
Deposition date deposition_date	2022-06-24
Structure title title	14-3-3 epsilon bound to phosphorylated PEAK2 (pS826) peptide
Keywords keywords	signaling protein; SIGNALING PROTEIN
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	18.60 Å
Radius of gyration Rg (electron density) rg_electron	17.52 Å
Forward intensity I(0) i0	8743740.00
Molecular weight molecular_weight	21429.0 kDa
Excluded volume excluded_volume	26658 Å³
Envelope volume envelope_volume	31297 Å³
Hydration-shell volume shell_volume	15544 Å³
Envelope diameter envelope_diameter	69.3 Å
Shell Rg shell_rg	23.25 Å
Envelope Rg envelope_rg	18.04 Å
Shape Rg shape_rg	17.53 Å
Total Rg total_rg	18.42 Å
Total atoms total_atoms	1510
Residues n_residues	203
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	67.9 Å
Rg (real space) rg_real	18.62 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	8.7440e+06
I(0) uncertainty (real space) i0_real_error	1.1550e+05
Rg (reciprocal space) rg_reciprocal	18.62 Å
I(0) (reciprocal space) i0_reciprocal	8744000.0000
Solution quality estimate total_estimate	0.8329
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.450
Kurtosis Kurtosis kurtosis	0.051
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1546000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.636; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	14-3-3 protein epsilon
Molecular weight formula_weight	29454.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1510

GSTMDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ

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	Phosphorylated PEAK2 (pS826) peptide
Molecular weight formula_weight	2175.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PPPLPQKKIVSRAASSPDGF

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8. Citations (1)

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Unit-cell length a length_a	92.131 Å
Unit-cell length b length_b	92.131 Å
Unit-cell length c length_c	137.439 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	3.160 Å
Low-resolution limit resolution_low	46.070 Å
R factor r_factor	0.2471
R_work r_work	0.2417
R_free r_free	0.2949

fit	/app/data/saxs_computation/dg/8dgn/8dgn.fit
pddf	/app/data/pr_computation/dg/8dgn/8dgn.pr.out
profile	/app/data/saxs_computation/dg/8dgn/8dgn.dat

14-3-3 epsilon bound to phosphorylated PEAK2 (pS826) 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)