9HDF | pdb_00009hdf

Glucocorticoid Receptor Ligand Binding Domain in complex with dexamethasone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

The multimerization pathway of the glucocorticoid receptor.

Alegre-Marti, A.Jimenez-Panizo, A.Lafuente, A.L.Johnson, T.A.Montoya-Novoa, I.Peralta-Moreno, M.N.Montanya-Valluguera, P.Ponseti-Pons, J.Abella, M.Kim, S.Diaz, M.Vilaseca, M.Perez, P.Fernandez-Recio, J.Rubio-Martinez, J.Presman, D.M.Hager, G.L.Fuentes-Prior, P.Estebanez-Perpina, E.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf1003
  • Primary Citation of Related Structures:  
    9HDF

  • PubMed Abstract: 

    The glucocorticoid receptor (GR) is a leading drug target due to its antiinflammatory and immunosuppressive roles. The functional oligomeric conformation of full-length GR (FL-GR), which is key for its biological activity, remains disputed. Here we present a new crystal structure of agonist-bound GR ligand-binding domain (GR-LBD) comprising eight copies of a noncanonical dimer. We verified the biological relevance of this dimer for receptor multimerization in wild-type and selected FL-GR mutants using molecular dynamics and crosslinking-mass spectrometry together with fluorescence microscopy and transcriptomic analysis in living cells. Self-association of this GR-LBD basic dimer in two mutually exclusive assemblies reveals clues for FL-GR multimerization and activity in cells. We propose a model for the structure of multidomain GR based on our new data and suggest a detailed oligomerization pathway. This model reconciles all currently available structural and functional information and provides a more comprehensive understanding of the rare disorder, generalized glucocorticoid resistance.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), Barcelona 08028, Spain.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ancestral Glucocorticoid Receptor2 ligand binding domain
A, C, D, F, G
A, C, D, F, G, H, I, L, M, P
248Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ancestral Glucocorticoid Receptor2 ligand binding domain
B, E, J, K, N
B, E, J, K, N, O
248Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 0 group B member 215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15466 (Homo sapiens)
Explore Q15466 
Go to UniProtKB:  Q15466
PHAROS:  Q15466
GTEx:  ENSG00000131910 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15466
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DEX
Query on DEX

Download Ideal Coordinates CCD File 
AD [auth M]
EB [auth D]
EC [auth J]
GA [auth A]
GD [auth N]
AD [auth M],
EB [auth D],
EC [auth J],
GA [auth A],
GD [auth N],
IB [auth E],
KD [auth O],
NA [auth B],
NC [auth K],
OD [auth P],
PB [auth F],
RC [auth L],
TB [auth G],
VB [auth H],
WA [auth C],
XB [auth I]
DEXAMETHASONE
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N
EPE
Query on EPE

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AC [auth I]
FC [auth J]
GB [auth D]
IA [auth A]
PA [auth B]
AC [auth I],
FC [auth J],
GB [auth D],
IA [auth A],
PA [auth B],
PD [auth P],
TC [auth L]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4
Query on PG4

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FB [auth D],
OA [auth B],
SC [auth L],
WB [auth H]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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CD [auth M]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CAC
Query on CAC

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BD [auth M]
DB [auth D]
HA [auth A]
JB [auth E]
LD [auth O]
BD [auth M],
DB [auth D],
HA [auth A],
JB [auth E],
LD [auth O],
OC [auth K],
UB [auth H],
YB [auth I]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
PEG
Query on PEG

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DD [auth M],
MC [auth K],
QB [auth F],
ZB [auth I]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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AB [auth C],
BB [auth C],
DC [auth J],
LA [auth A],
TA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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BC [auth I]
GC [auth J]
HC [auth J]
HD [auth N]
IC [auth J]
BC [auth I],
GC [auth J],
HC [auth J],
HD [auth N],
IC [auth J],
JA [auth A],
KA [auth A],
KB [auth E],
LB [auth E],
MB [auth E],
MD [auth O],
PC [auth K],
QA [auth B],
QC [auth K],
QD [auth P],
UC [auth L],
VC [auth L],
XA [auth C],
YA [auth C],
ZC [auth M]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

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CC [auth I]
ED [auth M]
ID [auth N]
JC [auth J]
KC [auth J]
CC [auth I],
ED [auth M],
ID [auth N],
JC [auth J],
KC [auth J],
NB [auth E],
ND [auth O],
RA [auth B],
RB [auth F],
RD [auth b],
SA [auth B],
SD [auth d],
WC [auth L],
XC [auth L],
ZA [auth C]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CL
Query on CL

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CB [auth C]
FD [auth M]
HB [auth D]
JD [auth N]
LC [auth J]
CB [auth C],
FD [auth M],
HB [auth D],
JD [auth N],
LC [auth J],
MA [auth B],
OB [auth E],
SB [auth F],
UA [auth B],
VA [auth B],
YC [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
B, E, J, K, N
B, E, J, K, N, O
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.41α = 90
b = 265.464β = 90
c = 109.671γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release