9HDF | pdb_00009hdf

Glucocorticoid Receptor Ligand Binding Domain in complex with dexamethasone

PDB DOI: https://doi.org/10.2210/pdb9HDF/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-12 Released: 2025-11-12
Deposition Author(s): Alegre-Marti, A., Jimenez-Panizo, A., Fuentes-Prior, P., Estebanez-Perpina, E.
Funding Organization(s): Not funded

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

PubMed: 41118578 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkaf1003
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 497.63 kDa
Atom Count: 34,585
Modeled Residue Count: 4,169
Deposited Residue Count: 4,208
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral Glucocorticoid Receptor2 ligand binding domain	A, C, D, F, G A, C, D, F, G, H, I, L, M, P	248	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral Glucocorticoid Receptor2 ligand binding domain	B, E, J, K, N B, E, J, K, N, O	248	Homo sapiens	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 0 group B member 2	AA [auth k] BA [auth l] CA [auth m] DA [auth n] EA [auth o] AA [auth k], BA [auth l], CA [auth m], DA [auth n], EA [auth o], FA [auth p], Q [auth a], R [auth b], S [auth c], T [auth d], U [auth e], V [auth f], W [auth g], X [auth h], Y [auth i], Z [auth j]	15	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15466
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DEX Query on DEX Download:Ideal Coordinates CCD File SDF format, chain AD [auth M] SDF format, chain EB [auth D] SDF format, chain EC [auth J] SDF format, chain GA [auth A] SDF format, chain KD [auth O] SDF format, chain NA [auth B] SDF format, chain NC [auth K] SDF format, chain OD [auth P] SDF format, chain PB [auth F] SDF format, chain RC [auth L] SDF format, chain TB [auth G] SDF format, chain VB [auth H] SDF format, chain XB [auth I] SDF format, chain WA [auth C] SDF format, chain IB [auth E] SDF format, chain GD [auth N] MOL2 format, chain AD [auth M] MOL2 format, chain EB [auth D] MOL2 format, chain EC [auth J] MOL2 format, chain GA [auth A] MOL2 format, chain KD [auth O] MOL2 format, chain NA [auth B] MOL2 format, chain NC [auth K] MOL2 format, chain OD [auth P] MOL2 format, chain PB [auth F] MOL2 format, chain RC [auth L] MOL2 format, chain TB [auth G] MOL2 format, chain VB [auth H] MOL2 format, chain XB [auth I] MOL2 format, chain WA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain GD [auth N] mmCIF format, chain AD [auth M] mmCIF format, chain EB [auth D] mmCIF format, chain EC [auth J] mmCIF format, chain GA [auth A] mmCIF format, chain KD [auth O] mmCIF format, chain NA [auth B] mmCIF format, chain NC [auth K] mmCIF format, chain OD [auth P] mmCIF format, chain PB [auth F] mmCIF format, chain RC [auth L] mmCIF format, chain TB [auth G] mmCIF format, chain VB [auth H] mmCIF format, chain XB [auth I] mmCIF format, chain WA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain GD [auth N]	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		Interactions Focus chain AD [auth M] Focus chain EB [auth D] Focus chain EC [auth J] Focus chain GA [auth A] Focus chain GD [auth N] Focus chain IB [auth E] Focus chain KD [auth O] Focus chain NA [auth B] Focus chain NC [auth K] Focus chain OD [auth P] Focus chain PB [auth F] Focus chain RC [auth L] Focus chain TB [auth G] Focus chain VB [auth H] Focus chain WA [auth C] Focus chain XB [auth I] Interactions & Density Focus chain AD [auth M] Focus chain EB [auth D] Focus chain EC [auth J] Focus chain GA [auth A] Focus chain GD [auth N] Focus chain IB [auth E] Focus chain KD [auth O] Focus chain NA [auth B] Focus chain NC [auth K] Focus chain OD [auth P] Focus chain PB [auth F] Focus chain RC [auth L] Focus chain TB [auth G] Focus chain VB [auth H] Focus chain WA [auth C] Focus chain XB [auth I]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain AC [auth I] SDF format, chain FC [auth J] SDF format, chain GB [auth D] SDF format, chain IA [auth A] SDF format, chain PA [auth B] SDF format, chain PD [auth P] SDF format, chain TC [auth L] MOL2 format, chain AC [auth I] MOL2 format, chain FC [auth J] MOL2 format, chain GB [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PD [auth P] MOL2 format, chain TC [auth L] mmCIF format, chain AC [auth I] mmCIF format, chain FC [auth J] mmCIF format, chain GB [auth D] mmCIF format, chain IA [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain PD [auth P] mmCIF format, chain TC [auth L]	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		Interactions Focus chain AC [auth I] Focus chain FC [auth J] Focus chain GB [auth D] Focus chain IA [auth A] Focus chain PA [auth B] Focus chain PD [auth P] Focus chain TC [auth L] Interactions & Density Focus chain AC [auth I] Focus chain FC [auth J] Focus chain GB [auth D] Focus chain IA [auth A] Focus chain PA [auth B] Focus chain PD [auth P] Focus chain TC [auth L]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain FB [auth D] SDF format, chain SC [auth L] SDF format, chain WB [auth H] SDF format, chain OA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain SC [auth L] MOL2 format, chain WB [auth H] MOL2 format, chain OA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain SC [auth L] mmCIF format, chain WB [auth H] mmCIF format, chain OA [auth B]	FB [auth D], OA [auth B], SC [auth L], WB [auth H]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain FB [auth D] Focus chain OA [auth B] Focus chain SC [auth L] Focus chain WB [auth H] Interactions & Density Focus chain FB [auth D] Focus chain OA [auth B] Focus chain SC [auth L] Focus chain WB [auth H]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain CD [auth M] MOL2 format, chain CD [auth M] mmCIF format, chain CD [auth M]	CD [auth M]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CD [auth M] Interactions & Density Focus chain CD [auth M]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain BD [auth M] SDF format, chain HA [auth A] SDF format, chain JB [auth E] SDF format, chain OC [auth K] SDF format, chain UB [auth H] SDF format, chain YB [auth I] SDF format, chain LD [auth O] SDF format, chain DB [auth D] MOL2 format, chain BD [auth M] MOL2 format, chain HA [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain OC [auth K] MOL2 format, chain UB [auth H] MOL2 format, chain YB [auth I] MOL2 format, chain LD [auth O] MOL2 format, chain DB [auth D] mmCIF format, chain BD [auth M] mmCIF format, chain HA [auth A] mmCIF format, chain JB [auth E] mmCIF format, chain OC [auth K] mmCIF format, chain UB [auth H] mmCIF format, chain YB [auth I] mmCIF format, chain LD [auth O] mmCIF format, chain DB [auth D]	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		Interactions Focus chain BD [auth M] Focus chain DB [auth D] Focus chain HA [auth A] Focus chain JB [auth E] Focus chain LD [auth O] Focus chain OC [auth K] Focus chain UB [auth H] Focus chain YB [auth I] Interactions & Density Focus chain BD [auth M] Focus chain DB [auth D] Focus chain HA [auth A] Focus chain JB [auth E] Focus chain LD [auth O] Focus chain OC [auth K] Focus chain UB [auth H] Focus chain YB [auth I]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain DD [auth M] SDF format, chain QB [auth F] SDF format, chain ZB [auth I] SDF format, chain MC [auth K] MOL2 format, chain DD [auth M] MOL2 format, chain QB [auth F] MOL2 format, chain ZB [auth I] MOL2 format, chain MC [auth K] mmCIF format, chain DD [auth M] mmCIF format, chain QB [auth F] mmCIF format, chain ZB [auth I] mmCIF format, chain MC [auth K]	DD [auth M], MC [auth K], QB [auth F], ZB [auth I]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DD [auth M] Focus chain MC [auth K] Focus chain QB [auth F] Focus chain ZB [auth I] Interactions & Density Focus chain DD [auth M] Focus chain MC [auth K] Focus chain QB [auth F] Focus chain ZB [auth I]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain DC [auth J] SDF format, chain LA [auth A] SDF format, chain TA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain DC [auth J] MOL2 format, chain LA [auth A] MOL2 format, chain TA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain DC [auth J] mmCIF format, chain LA [auth A] mmCIF format, chain TA [auth B]	AB [auth C], BB [auth C], DC [auth J], LA [auth A], TA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain DC [auth J] Focus chain LA [auth A] Focus chain TA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain DC [auth J] Focus chain LA [auth A] Focus chain TA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BC [auth I] SDF format, chain GC [auth J] SDF format, chain HC [auth J] SDF format, chain HD [auth N] SDF format, chain IC [auth J] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LB [auth E] SDF format, chain MB [auth E] SDF format, chain PC [auth K] SDF format, chain QA [auth B] SDF format, chain QC [auth K] SDF format, chain QD [auth P] SDF format, chain UC [auth L] SDF format, chain VC [auth L] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZC [auth M] SDF format, chain MD [auth O] SDF format, chain KB [auth E] MOL2 format, chain BC [auth I] MOL2 format, chain GC [auth J] MOL2 format, chain HC [auth J] MOL2 format, chain HD [auth N] MOL2 format, chain IC [auth J] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain PC [auth K] MOL2 format, chain QA [auth B] MOL2 format, chain QC [auth K] MOL2 format, chain QD [auth P] MOL2 format, chain UC [auth L] MOL2 format, chain VC [auth L] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZC [auth M] MOL2 format, chain MD [auth O] MOL2 format, chain KB [auth E] mmCIF format, chain BC [auth I] mmCIF format, chain GC [auth J] mmCIF format, chain HC [auth J] mmCIF format, chain HD [auth N] mmCIF format, chain IC [auth J] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LB [auth E] mmCIF format, chain MB [auth E] mmCIF format, chain PC [auth K] mmCIF format, chain QA [auth B] mmCIF format, chain QC [auth K] mmCIF format, chain QD [auth P] mmCIF format, chain UC [auth L] mmCIF format, chain VC [auth L] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZC [auth M] mmCIF format, chain MD [auth O] mmCIF format, chain KB [auth E]	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		Interactions Focus chain BC [auth I] Focus chain GC [auth J] Focus chain HC [auth J] Focus chain HD [auth N] Focus chain IC [auth J] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain MD [auth O] Focus chain PC [auth K] Focus chain QA [auth B] Focus chain QC [auth K] Focus chain QD [auth P] Focus chain UC [auth L] Focus chain VC [auth L] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZC [auth M] Interactions & Density Focus chain BC [auth I] Focus chain GC [auth J] Focus chain HC [auth J] Focus chain HD [auth N] Focus chain IC [auth J] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain MD [auth O] Focus chain PC [auth K] Focus chain QA [auth B] Focus chain QC [auth K] Focus chain QD [auth P] Focus chain UC [auth L] Focus chain VC [auth L] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZC [auth M]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain CC [auth I] SDF format, chain ED [auth M] SDF format, chain ID [auth N] SDF format, chain JC [auth J] SDF format, chain NB [auth E] SDF format, chain RA [auth B] SDF format, chain RB [auth F] SDF format, chain RD [auth b] SDF format, chain SA [auth B] SDF format, chain SD [auth d] SDF format, chain WC [auth L] SDF format, chain XC [auth L] SDF format, chain ZA [auth C] SDF format, chain ND [auth O] SDF format, chain KC [auth J] MOL2 format, chain CC [auth I] MOL2 format, chain ED [auth M] MOL2 format, chain ID [auth N] MOL2 format, chain JC [auth J] MOL2 format, chain NB [auth E] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth F] MOL2 format, chain RD [auth b] MOL2 format, chain SA [auth B] MOL2 format, chain SD [auth d] MOL2 format, chain WC [auth L] MOL2 format, chain XC [auth L] MOL2 format, chain ZA [auth C] MOL2 format, chain ND [auth O] MOL2 format, chain KC [auth J] mmCIF format, chain CC [auth I] mmCIF format, chain ED [auth M] mmCIF format, chain ID [auth N] mmCIF format, chain JC [auth J] mmCIF format, chain NB [auth E] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth F] mmCIF format, chain RD [auth b] mmCIF format, chain SA [auth B] mmCIF format, chain SD [auth d] mmCIF format, chain WC [auth L] mmCIF format, chain XC [auth L] mmCIF format, chain ZA [auth C] mmCIF format, chain ND [auth O] mmCIF format, chain KC [auth J]	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		Interactions Focus chain CC [auth I] Focus chain ED [auth M] Focus chain ID [auth N] Focus chain JC [auth J] Focus chain KC [auth J] Focus chain NB [auth E] Focus chain ND [auth O] Focus chain RA [auth B] Focus chain RB [auth F] Focus chain RD [auth b] Focus chain SA [auth B] Focus chain SD [auth d] Focus chain WC [auth L] Focus chain XC [auth L] Focus chain ZA [auth C] Interactions & Density Focus chain CC [auth I] Focus chain ED [auth M] Focus chain ID [auth N] Focus chain JC [auth J] Focus chain KC [auth J] Focus chain NB [auth E] Focus chain ND [auth O] Focus chain RA [auth B] Focus chain RB [auth F] Focus chain RD [auth b] Focus chain SA [auth B] Focus chain SD [auth d] Focus chain WC [auth L] Focus chain XC [auth L] Focus chain ZA [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain FD [auth M] SDF format, chain HB [auth D] SDF format, chain JD [auth N] SDF format, chain LC [auth J] SDF format, chain MA [auth B] SDF format, chain OB [auth E] SDF format, chain SB [auth F] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain YC [auth L] MOL2 format, chain CB [auth C] MOL2 format, chain FD [auth M] MOL2 format, chain HB [auth D] MOL2 format, chain JD [auth N] MOL2 format, chain LC [auth J] MOL2 format, chain MA [auth B] MOL2 format, chain OB [auth E] MOL2 format, chain SB [auth F] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain YC [auth L] mmCIF format, chain CB [auth C] mmCIF format, chain FD [auth M] mmCIF format, chain HB [auth D] mmCIF format, chain JD [auth N] mmCIF format, chain LC [auth J] mmCIF format, chain MA [auth B] mmCIF format, chain OB [auth E] mmCIF format, chain SB [auth F] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain YC [auth L]	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		Interactions Focus chain CB [auth C] Focus chain FD [auth M] Focus chain HB [auth D] Focus chain JD [auth N] Focus chain LC [auth J] Focus chain MA [auth B] Focus chain OB [auth E] Focus chain SB [auth F] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain YC [auth L] Interactions & Density Focus chain CB [auth C] Focus chain FD [auth M] Focus chain HB [auth D] Focus chain JD [auth N] Focus chain LC [auth J] Focus chain MA [auth B] Focus chain OB [auth E] Focus chain SB [auth F] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain YC [auth L]