1A28

HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Atomic structure of progesterone complexed with its receptor.

Williams, S.P.Sigler, P.B.

(1998) Nature 393: 392-396

  • DOI: 10.1038/30775
  • Primary Citation of Related Structures:  
    1A28

  • PubMed Abstract: 
  • The physiological effects of progestins are mediated by the progesterone receptor, a member of the steroid/nuclear receptor superfamily. As progesterone is required for maintenance of pregnancy, its receptor has been a target for pharmaceuticals. Here we report the 1 ...

    The physiological effects of progestins are mediated by the progesterone receptor, a member of the steroid/nuclear receptor superfamily. As progesterone is required for maintenance of pregnancy, its receptor has been a target for pharmaceuticals. Here we report the 1.8 A crystal structure of a progesterone-bound ligand-binding domain of the human progesterone receptor. The nature of this structure explains the receptor's selective affinity for progestins and establishes a common mode of recognition of 3-oxy steroids by the cognate receptors. Although the overall fold of the progesterone receptor is similar to that found in related receptors, the progesterone receptor has a quite different mode of dimerization. A hormone-induced stabilization of the carboxy-terminal secondary structure of the ligand-binding domain of the progesterone receptor accounts for the stereochemistry of this distinctive dimer, explains the receptor's characteristic pattern of ligand-dependent protease resistance and its loss of repression, and indicates how the anti-progestin RU486 might work in birth control. The structure also indicates that the analogous 3-keto-steroid receptors may have a similar mechanism of action.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, and the Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06510, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROGESTERONE RECEPTORA, B256Homo sapiensMutation(s): 0 
Gene Names: PGRNR3C3
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
PHAROS:  P06401
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STR (Subject of Investigation/LOI)
Query on STR

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]PROGESTERONE
C21 H30 O2
RJKFOVLPORLFTN-LEKSSAKUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
STR PDBBind:  1A28 Ki: 5.1 (nM) from 1 assay(s)
Binding MOAD:  1A28 Ki: 5.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.123α = 90
b = 64.444β = 95.74
c = 69.954γ = 90
Software Package:
Software NamePurpose
DPHASEmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DPHASEphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance