3o8i

Structure of 14-3-3 isoform sigma in complex with a C-Raf1 peptide and a stabilizing small molecule fragment

Method: X-RAY DIFFRACTION Dmax: 64.0 Å Quality: REASONABLE

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

14-3-3 protein sigma

Homo sapiens

UniProt P31947

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 1–231 Fragment:C-terminal deletion 14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase × 2 (P04049) M1T 6,6-dihydroxy-1-methoxyhexan-2-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277.15 K;0.095M HEPES Na, 26.6%(v/v) PEG400, 0.19M CaCl2, 5%(v/v) Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K Resolution 2.00 Å R-free 0.239

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.

523 other PDB entries and 543 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433S_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–239; UniProt 1–231

14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase

OrganismNot specified

UniProt P04049

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 B; UniProt 255–264 Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein sigma × 2 (P31947) M1T 6,6-dihydroxy-1-methoxyhexan-2-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277.15 K;0.095M HEPES Na, 26.6%(v/v) PEG400, 0.19M CaCl2, 5%(v/v) Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K Resolution 2.00 Å R-free 0.239

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.

74 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAF1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–10; UniProt 255–264

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 3o8i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3o8i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3o8i
Deposition date deposition_date2010-08-03
Structure title titleStructure of 14-3-3 isoform sigma in complex with a C-Raf1 peptide and a stabilizing small molecule fragment
Keywords keywordsProtein-Protein Complex, 14-3-3, Protein-protein interaction, Phosphorylation, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.53
Radius of gyration Rg (electron density) rg_electron18.43
Forward intensity I(0) i012287400.00
Molecular weight molecular_weight25650.0 kDa
Excluded volume excluded_volume31961 ų
Envelope volume envelope_volume38728 ų
Hydration-shell volume shell_volume17864 ų
Envelope diameter envelope_diameter67.0
Shell Rg shell_rg24.41
Envelope Rg envelope_rg18.74
Shape Rg shape_rg18.42
Total Rg total_rg19.37
Total atoms total_atoms1796
Residues n_residues225
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 dmax64.0
Rg (real space) rg_real19.45
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real1.2290e+07
I(0) uncertainty (real space) i0_real_error1.5100e+05
Rg (reciprocal space) rg_reciprocal19.46
I(0) (reciprocal space) i0_reciprocal12290000.0000
Solution quality estimate total_estimate0.6752
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.4
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.374
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3060000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 0.998; Sysdev: 0.424; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3o8ia1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.7 — 14-3-3 protein
Family Family familya.118.7.1 — 14-3-3 protein
Domain ID domain_idd3o8ia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id3o8iA00
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)