9EBL | pdb_00009ebl

Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 1)

• PDB DOI: https://doi.org/10.2210/pdb9EBL/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-12 Released: 2025-11-19 
• Deposition Author(s): Pederick, J.L., Bruning, J.B.
• Funding Organization(s): Australian Research Council (ARC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the hERalpha LBD complexed with androstenediol and SRC 2-2 peptide

Pederick, J.L., Bruning, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A8B6C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A8B1C1D1E1F1G1H1I1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 115.46 kDa 
• Atom Count: 7,207 
• Modeled Residue Count: 921 
• Deposited Residue Count: 1,008 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B, E, F	239	Homo sapiens	Mutation(s): 0  Gene Names: ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C, D, G, H	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B81 (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth E], L [auth F]	(3alpha,8alpha,17beta)-androst-5-ene-3,17-diol C19 H30 O2 QADHLRWLCPCEKT-LOVVWNRFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.277 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.94	α = 90
b = 213.735	β = 98.66
c = 52.507	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Pederick, J.L., Bruning, J.B.

---

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP230100609

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release