3HM1

Crystal structure of human Estrogen Receptor Alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide and estrone ((8R,9S,13S,14S)-3-hydroxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one)

• PDB DOI: https://doi.org/10.2210/pdb3HM1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-05-28 Released: 2010-06-02 
• Deposition Author(s): Rajan, S.S., Kim, Y., Vanek, K., Liwanag, M., Joachimiak, A., Greene, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.289 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Crystal structure of human Estrogen Receptor Alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide and estrone ((8R,9S,13S,14S)-3-hydroxy-13-methyl-7,8,9,11,12,14,15, 16-octahydro-6H-cyclopenta[a]phenanthren-17-one)

Rajan, S.S., Kim, Y., Vanek, K., Joachimiak, A., Greene, G.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.04 kDa 
• Atom Count: 4,062 
• Modelled Residue Count: 493 
• Deposited Residue Count: 532 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	253	Homo sapiens	Mutation(s): 1  Gene Names: ESR, ESR1, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
GTEx:  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C, D	13	Rattus norvegicus	Mutation(s): 0  Gene Names: Ncoa2
UniProt
Find proteins for Q9WUI9 (Rattus norvegicus) Explore Q9WUI9  Go to UniProtKB:  Q9WUI9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J3Z	E [auth A], F [auth B]	(9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one C18 H22 O2 DNXHEGUUPJUMQT-CBZIJGRNSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
J3Z	BindingDB:  3HM1	IC50: min: 29, max: 480 (nM) from 4 assay(s)
		EC50: min: 0.7, max: 166 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.289 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.267	α = 90
b = 82.666	β = 109.18
c = 58.989	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
XFIT	data reduction
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Rajan, S.S., Kim, Y., Vanek, K., Liwanag, M., Joachimiak, A., Greene, G.L.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description