1YA3

Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to progesterone and harboring the S810L mutation responsible for a severe form of hypertension

• PDB DOI: https://doi.org/10.2210/pdb1YA3/pdb

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


• Deposited: 2004-12-17 Released: 2005-05-24 
• Deposition Author(s): Fagart, J., Huyet, J., Pinon, G.M., Rochel, M., Mayer, C., Rafestin-Oblin, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.284 
• R-Value Work: 0.237 
• R-Value Observed: 0.252 

Starting Model: experimental

Literature

Crystal structure of a mutant mineralocorticoid receptor responsible for hypertension

Fagart, J., Huyet, J., Pinon, G.M., Rochel, M., Mayer, C., Rafestin-Oblin, M.E.

(2005) Nat Struct Mol Biol 12: 554-555

• PubMed: 15908963 
• DOI: https://doi.org/10.1038/nsmb939
• Primary Citation of Related Structures:  
  1Y9R, 1YA3


• PubMed Abstract: 
  

  The S810L mutation within the human mineralocorticoid receptor (MR S810L) induces severe hypertension and switches progesterone from antagonist to agonist. Here we report the crystal structures of the ligand-binding domain of MR S810L in complex with progesterone and deoxycorticosterone, an agonist of both wild-type and mutant MRs. These structures, the first for MR, identify the specific contacts created by Leu810 and clarify the mechanism of activation of MR S810L.

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Organizational Affiliation: 

INSERM U478, Faculté de Médecine Xavier Bichat, 16 rue Henri Huchard, B.P. 416, 75870 Paris Cedex 18, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.88 kDa 
• Atom Count: 5,764 
• Modelled Residue Count: 695 
• Deposited Residue Count: 765 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mineralocorticoid receptor	A, B, C	255	Homo sapiens	Mutation(s): 2  Gene Names: NR3C2, MCR, MLR
UniProt & NIH Common Fund Data Resources
Find proteins for P08235 (Homo sapiens) Explore P08235  Go to UniProtKB:  P08235
PHAROS:  P08235 GTEx:  ENSG00000151623

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STR	D [auth A], E [auth B], F [auth C]	PROGESTERONE C21 H30 O2 RJKFOVLPORLFTN-LEKSSAKUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STR	BindingDB:  1YA3	Kd: 0.39 (nM) from 1 assay(s)
		IC50: min: 14, max: 30 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.284 
• R-Value Work: 0.237 
• R-Value Observed: 0.252 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.7237	α = 90
b = 120.7237	β = 90
c = 42.5081	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
BEAST	model building
CNS	refinement
CCP4	data scaling
BEAST	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-24 
Deposition Author(s): Fagart, J., Huyet, J., Pinon, G.M., Rochel, M., Mayer, C., Rafestin-Oblin, M.E.

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description