9MDV | pdb_00009mdv

Apo form of the estrogen receptor alpha ligand binding domain of Melanotaenia fluviatilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.286 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A ternary switch model governing ER alpha ligand binding domain conformation.

McDougal, D.P.Pederick, J.L.Novick, S.J.Jovcevski, B.Warrender, A.K.Pascal, B.D.Griffin, P.R.Bruning, J.B.

(2025) Nat Commun 16: 10363-10363

  • DOI: https://doi.org/10.1038/s41467-025-65323-9
  • Primary Citation of Related Structures:  
    9MDV

  • PubMed Abstract: 

    The transcription factor estrogen receptor α is the primary driver of ER+ breast cancer progression and a target of multiple FDA-approved anticancer drugs. Ligand-dependent activity of ERα is determined by helix-12 conformation within the ligand binding domain. However, how helix-12 transitions from an unliganded (apo) state to active (estrogen-bound) or inactive (SERM/SERD-bound) states remains unresolved. Here, we present the crystal structure of an apo estrogen receptor α ligand binding domain from the teleost Melanotaenia fluviatilis, revealing a third distinct helix-12 conformation. Structural mass spectrometry and molecular dynamics simulations reveal that apo helix-12 is maintained in a stable and distinct conformation prior to ligand binding. Clashes between ligand and evolutionarily conserved residues L525, L536 and L540 displace helix-12, to promote activation or inactivation of the receptor. The crystal structure further reveals that breast cancer-associated mutations, Y537S and D538G, disrupt residue contacts critical for stabilising apo helix-12 conformation. We propose a model whereby helix-12 functions as a ternary molecular switch to determine receptor activity. These findings provide critical insights into the ligand-dependent and -independent regulation of estrogen receptor α and have significant implications for therapeutic intervention.


  • Organizational Affiliation
    • Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
251Melanotaenia fluviatilisMutation(s): 0 
Gene Names: ESR1
UniProt
Find proteins for D6N7U3 (Melanotaenia fluviatilis)
Explore D6N7U3 
Go to UniProtKB:  D6N7U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6N7U3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.374α = 90
b = 94.507β = 96.86
c = 60.954γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP230100609

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references