8daf

Human SF-1 LBD bound to synthetic agonist 6N-10CA and bacterial phospholipid

Method: X-RAY DIFFRACTION Dmax: 93.7 Å Quality: GOOD

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

Steroidogenic factor 1

Homo sapiens

UniProt Q13285

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 218–461 Not recorded Nuclear receptor coactivator 2 × 1 (Q15596) IUW 10-[(3aR,6S,6aR)-3-phenyl-3a-(1-phenylethenyl)-6-(sulfamoylamino)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid (non-preferred name) × 1 PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;277.15 K;Na acetate (pH 4.6), glycerol, PEG 4000 Resolution 2.59 Å R-free 0.281
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 218–461 Not recorded Nuclear receptor coactivator 2 × 1 (Q15596) IUW 10-[(3aR,6S,6aR)-3-phenyl-3a-(1-phenylethenyl)-6-(sulfamoylamino)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid (non-preferred name) × 1 PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;277.15 K;Na acetate (pH 4.6), glycerol, PEG 4000 Resolution 2.59 Å R-free 0.281

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.

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–247; UniProt 218–461 Author chain B; PDBConstruct 4–247; UniProt 218–461

Nuclear receptor coactivator 2

Homo sapiens

UniProt Q15596

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 C; UniProt 740–753 Not recorded Steroidogenic factor 1 × 1 (Q13285) IUW 10-[(3aR,6S,6aR)-3-phenyl-3a-(1-phenylethenyl)-6-(sulfamoylamino)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid (non-preferred name) × 1 PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;277.15 K;Na acetate (pH 4.6), glycerol, PEG 4000 Resolution 2.59 Å R-free 0.281
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 740–753 Not recorded Steroidogenic factor 1 × 1 (Q13285) IUW 10-[(3aR,6S,6aR)-3-phenyl-3a-(1-phenylethenyl)-6-(sulfamoylamino)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid (non-preferred name) × 1 PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;277.15 K;Na acetate (pH 4.6), glycerol, PEG 4000 Resolution 2.59 Å R-free 0.281

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.

283 other PDB entries and 333 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCOA2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–14; UniProt 740–753 Author chain D; PDBConstruct 1–14; UniProt 740–753

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 8daf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8daf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8daf
Deposition date deposition_date2022-06-13
Structure title titleHuman SF-1 LBD bound to synthetic agonist 6N-10CA and bacterial phospholipid
Keywords keywordsSF-1, Nuclear Receptor, Ligand, Synthetic Agonist, NUCLEAR PROTEIN, Steroidogenic factor-1, NR5A1; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.21
Radius of gyration Rg (electron density) rg_electron29.66
Forward intensity I(0) i048723100.00
Molecular weight molecular_weight57092.0 kDa
Excluded volume excluded_volume72596 ų
Envelope volume envelope_volume94194 ų
Hydration-shell volume shell_volume26649 ų
Envelope diameter envelope_diameter94.0
Shell Rg shell_rg36.52
Envelope Rg envelope_rg28.97
Shape Rg shape_rg29.67
Total Rg total_rg30.36
Total atoms total_atoms8117
Residues n_residues488
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 dmax93.7
Rg (real space) rg_real30.26
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real4.8720e+07
I(0) uncertainty (real space) i0_real_error6.7090e+05
Rg (reciprocal space) rg_reciprocal30.24
I(0) (reciprocal space) i0_reciprocal48720000.0000
Solution quality estimate total_estimate0.8144
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.2
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.836
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15260000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (4)

9. Files and Curves (10)