6a5q

Structure of 14-3-3 beta in complex with TFEB 14-3-3 binding motif

Method: X-RAY DIFFRACTION Dmax: 104.0 Å Quality: EXCELLENT

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

14-3-3 protein beta/alpha

Homo sapiens

UniProt P31946

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 1–246 Chain B; UniProt 1–246 Not recorded TFEB pS211-peptide × 2 MLA MALONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 4;289 K;0.1 M sodium malonate, and 12% (w/v) PEG 3350 Resolution 2.00 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–246 Not recorded TFEB pS211-peptide × 2 MLA MALONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 4;289 K;0.1 M sodium malonate, and 12% (w/v) PEG 3350 Resolution 2.00 Å R-free 0.230

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.

16 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–250; UniProt 1–246 Author chain B; PDBConstruct 5–250; UniProt 1–246 Author chain C; PDBConstruct 5–250; UniProt 1–246

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 6a5q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a5q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6a5q
Deposition date deposition_date2018-06-25
Structure title titleStructure of 14-3-3 beta in complex with TFEB 14-3-3 binding motif
Keywords keywordsPHOSPHOSERIN, REGULATION, TRANSCRIPTION FACTOR, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.52
Radius of gyration Rg (electron density) rg_electron31.92
Forward intensity I(0) i0115163000.00
Molecular weight molecular_weight82907.0 kDa
Excluded volume excluded_volume102800 ų
Envelope volume envelope_volume135150 ų
Hydration-shell volume shell_volume36132 ų
Envelope diameter envelope_diameter105.5
Shell Rg shell_rg38.05
Envelope Rg envelope_rg31.32
Shape Rg shape_rg31.91
Total Rg total_rg32.44
Total atoms total_atoms5810
Residues n_residues724
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax104.0
Rg (real space) rg_real32.42
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real1.1520e+08
I(0) uncertainty (real space) i0_real_error1.7780e+06
Rg (reciprocal space) rg_reciprocal32.46
I(0) (reciprocal space) i0_reciprocal115200000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.5
Skewness Skewness skewness0.156
Kurtosis Kurtosis kurtosis-0.585
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14190000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.932

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6a5qA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain
Domain ID domain_id6a5qB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain
Domain ID domain_id6a5qC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain

8. Citations (1)

9. Files and Curves (10)