9D8Q | pdb_00009d8q

Crystal structure of Estrogen Receptor alpha from Melanotaenia fluviatilis bound to estradiol and human SRC2 peptide

PDB DOI: https://doi.org/10.2210/pdb9D8Q/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Melanotaenia fluviatilis, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-20 Released: 2025-10-22
Deposition Author(s): McDougal, D.P., Pederick, J.L., Bruning, J.B.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.261 (Depositor), 0.265 (DCC)
R-Value Work:
0.226 (Depositor), 0.228 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of constraint in estrogen receptors

McDougal, D.P., Pederick, J.L., Shearwin-Whyatt, L., Grutzner, F., Bruning, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 30.44 kDa
Atom Count: 1,912
Modeled Residue Count: 241
Deposited Residue Count: 263
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	250	Melanotaenia fluviatilis	Mutation(s): 0 Gene Names: ESR1
UniProt
Find proteins for D6N7U3 (Melanotaenia fluviatilis) Explore D6N7U3 Go to UniProtKB: D6N7U3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D6N7U3
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	B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EST (Subject of Investigation/LOI) Query on EST Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ESTRADIOL C₁₈ H₂₄ O₂ VOXZDWNPVJITMN-ZBRFXRBCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.261 (Depositor), 0.265 (DCC)
R-Value Work: 0.226 (Depositor), 0.228 (DCC)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.184	α = 90
b = 167.184	β = 90
c = 167.184	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.