4UDC

GR in complex with dexamethasone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints.

Edman, K., Hosseini, A., Bjursell, M.K., Aagaard, A., Wissler, L., Gunnarsson, A., Kaminski, T., Kohler, C., Backstrom, S., Jensen, T.J., Cavallin, A., Karlsson, U., Nilsson, E., Lecina, D., Takahashi, R., Grebner, C., Geschwindner, S., Lepisto, M., Hogner, A.C., Guallar, V.

(2015) Structure 23: 2280

  • DOI: 10.1016/j.str.2015.09.012
  • Primary Citation of Related Structures:  
    4UDA, 4UDB, 4UDC, 4UDD

  • PubMed Abstract: 

    • Steroid receptor drugs have been available for more than half a century, but details of the ligand binding mechanism have remained elusive. We solved X-ray structures of the glucocorticoid and mineralocorticoid receptors to identify a conserved plasticity at the helix 6-7 region that extends the ligand binding pocket toward the receptor surface ...

    Steroid receptor drugs have been available for more than half a century, but details of the ligand binding mechanism have remained elusive. We solved X-ray structures of the glucocorticoid and mineralocorticoid receptors to identify a conserved plasticity at the helix 6-7 region that extends the ligand binding pocket toward the receptor surface. Since none of the endogenous ligands exploit this region, we hypothesized that it constitutes an integral part of the binding event. Extensive all-atom unbiased ligand exit and entrance simulations corroborate a ligand binding pathway that gives the observed structural plasticity a key functional role. Kinetic measurements reveal that the receptor residence time correlates with structural rearrangements observed in both structures and simulations. Ultimately, our findings reveal why nature has conserved the capacity to open up this region, and highlight how differences in the details of the ligand entry process result in differential evolutionary constraints across the steroid receptors.

    Organizational Affiliation: 

    Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain. Electronic address: victor.guallar@bsc.es.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOCORTICOID RECEPTOR A280Homo sapiensMutation(s): 3 
Gene Names: NR3C1, GRL
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
NIH Common Fund Data Resources
PHAROS:  P04150
GTEx:  ENSG00000113580
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR RECEPTOR COACTIVATOR 2 B14Homo sapiensMutation(s): 0 
Gene Names: NCOA2, BHLHE75, SRC2, TIF2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596
GTEx:  ENSG00000140396
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS
Download Ideal Coordinates CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N		 Ligand Interaction
DEX
Query on DEX
Download Ideal Coordinates CCD File 
A
DEXAMETHASONE
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.66α = 90
b = 84.66β = 90
c = 105.91γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy