4zn9

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with Oxabicyclic Heptene Sulfonate (OBHS)

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: EXCELLENT

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

Estrogen receptor

Homo sapiens

UniProt P03372

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 301–559 Chain B; UniProt 301–559 Fragment:ligand-binding domain, UNP residues 301-559 Mutation:Y537S Nuclear receptor-interacting peptide × 2 (Q15596) OBH cyclohexa-2,5-dien-1-yl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.3;294 K;15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris Resolution 2.21 Å R-free 0.242

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.

434 other PDB entries and 522 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ESR1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–259; UniProt 301–559 Author chain B; PDBConstruct 1–259; UniProt 301–559

Nuclear receptor-interacting peptide

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 C; UniProt 686–698 Chain D; UniProt 686–698 Fragment:UNP residues 686-698 Estrogen receptor × 2 (P03372) OBH cyclohexa-2,5-dien-1-yl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.3;294 K;15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris Resolution 2.21 Å R-free 0.242

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 334 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

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 4zn9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zn9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zn9
Deposition date deposition_date2015-05-04
Structure title titleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with Oxabicyclic Heptene Sulfonate (OBHS)
Keywords keywordsprotein ligand complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.52
Radius of gyration Rg (electron density) rg_electron22.34
Forward intensity I(0) i049751000.00
Molecular weight molecular_weight56234.0 kDa
Excluded volume excluded_volume70998 ų
Envelope volume envelope_volume81955 ų
Hydration-shell volume shell_volume29388 ų
Envelope diameter envelope_diameter76.3
Shell Rg shell_rg30.14
Envelope Rg envelope_rg22.54
Shape Rg shape_rg22.36
Total Rg total_rg23.13
Total atoms total_atoms3934
Residues n_residues491
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 dmax71.8
Rg (real space) rg_real23.35
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real4.9750e+07
I(0) uncertainty (real space) i0_real_error6.0530e+05
Rg (reciprocal space) rg_reciprocal23.39
I(0) (reciprocal space) i0_reciprocal49750000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.8
Skewness Skewness skewness0.117
Kurtosis Kurtosis kurtosis-0.485
Angular range angular_range— – 0.3400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13880000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4zn9A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id4zn9B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor

8. Citations (2)

9. Files and Curves (10)