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.

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
PHAROS: P03372 GTEx: ENSG00000091831
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WUI9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J3Z Query on J3Z Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	(9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one C₁₈ H₂₂ O₂ DNXHEGUUPJUMQT-CBZIJGRNSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

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

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2024-11-20
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.