9ecf

Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2)

Method: X-RAY DIFFRACTION Dmax: 122.7 Å Quality: GOOD

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

Estrogen receptor beta

Homo sapiens

UniProt Q92731

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 E; UniProt 261–500 Chain F; UniProt 261–500 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 261–500 Chain B; UniProt 261–500 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 261–500 Chain J; UniProt 261–500 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain M; UniProt 261–500 Chain N; UniProt 261–500 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278

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.

36 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ESR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–247; UniProt 261–500 Author chain B; PDBConstruct 8–247; UniProt 261–500 Author chain E; PDBConstruct 8–247; UniProt 261–500 Author chain F; PDBConstruct 8–247; UniProt 261–500 Author chain I; PDBConstruct 8–247; UniProt 261–500 Author chain J; PDBConstruct 8–247; UniProt 261–500 Author chain M; PDBConstruct 8–247; UniProt 261–500 Author chain N; PDBConstruct 8–247; UniProt 261–500

Nuclear receptor coactivator 2

OrganismNot specified

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 686–698 Chain H; UniProt 686–698 Not recorded Estrogen receptor beta × 2 (Q92731) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 686–698 Chain D; UniProt 686–698 Not recorded Estrogen receptor beta × 2 (Q92731) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain K; UniProt 686–698 Chain L; UniProt 686–698 Not recorded Estrogen receptor beta × 2 (Q92731) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain O; UniProt 686–698 Chain P; UniProt 686–698 Not recorded Estrogen receptor beta × 2 (Q92731) B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289.15 K;0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 Resolution 2.00 Å R-free 0.278

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 331 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 1–13; UniProt 686–698 Author chain D; PDBConstruct 1–13; UniProt 686–698 Author chain G; PDBConstruct 1–13; UniProt 686–698 Author chain H; PDBConstruct 1–13; UniProt 686–698 Author chain K; PDBConstruct 1–13; UniProt 686–698 Author chain L; PDBConstruct 1–13; UniProt 686–698 Author chain O; PDBConstruct 1–13; UniProt 686–698 Author chain P; PDBConstruct 1–13; UniProt 686–698

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 9ecf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ecf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ecf
Deposition date deposition_date2024-11-14
最后修订 last_revision2025-11-19
Structure title titleCrystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2)
Keywords keywordsnuclear receptor, transcription factor, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.23
Radius of gyration Rg (electron density) rg_electron40.67
Forward intensity I(0) i0538202000.00
Molecular weight molecular_weight201020.0 kDa
Excluded volume excluded_volume256440 ų
Envelope volume envelope_volume336320 ų
Hydration-shell volume shell_volume67868 ų
Envelope diameter envelope_diameter127.8
Shell Rg shell_rg47.15
Envelope Rg envelope_rg39.86
Shape Rg shape_rg40.70
Total Rg total_rg40.91
Total atoms total_atoms14051
Residues n_residues1813
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 dmax122.7
Rg (real space) rg_real41.02
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real5.3820e+08
I(0) uncertainty (real space) i0_real_error7.2550e+06
Rg (reciprocal space) rg_reciprocal41.23
I(0) (reciprocal space) i0_reciprocal538300000.0000
Solution quality estimate total_estimate0.8931
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.4
Skewness Skewness skewness0.029
Kurtosis Kurtosis kurtosis-0.677
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha205400000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.715

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)