6W9L: Glucocorticoid Receptor

Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with deacetylated deflazacort and PGC1a coregulator fragment. Determined by X-ray diffraction at 1.45 Å resolution. Released 4 Nov 2020.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: synthetic construct, Homo sapiens
Chains: 2
Atoms: 2,400
Mol. weight: 30.54 kDa
Ligands: TUS
Released: 4 Nov 2020

Explore 6W9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9L contains 15 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	10-14	5
α-helix	22-23	2
α-helix	25-49	25
α-helix	53-55	3
α-helix	58-85	28
β-strand	90-93	4	1
β-strand	96-98	3	1
α-helix	101-103	3
α-helix	108-125	18
α-helix	129-140	12
β-strand	143-145	3	2
α-helix	152-172	21
α-helix	177-179	3
α-helix	180-210	31
α-helix	212-214	3
α-helix	220-234	15
β-strand	238-240	3	2

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	143-149	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glucocorticoid Receptor	A	protein	249	synthetic construct	A0A1X8XLE9 (AlphaFold model)
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B	protein	12	Homo sapiens	Q9UBK2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6W9L_1 Glucocorticoid Receptor (chains A)
FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLH
LDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLK
ISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNS
SQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGS
VKPLLFHQK

Sequence of entity 2 (B), FASTA

>6W9L_2 Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (chains B)
PSLLKKLLLAPA

Ligands and cofactors

ID	Name	Formula	Copies
TUS	(4aR,4bS,5S,6aS,6bS,9aR,10aS,10bS)-5-hydroxy-6b-(hydroxyacetyl)-4a,6a,8-trimeth…	C23 H29 N O5	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment. Liu, X., Wang, Y., Gutierrez, J.S. et al. Proc Natl Acad Sci U S A (2020) 117:24285-24293. DOI 10.1073/pnas.2006890117 · PubMed

Other PDB entries of the same protein (UniProt A0A1X8XLE9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W9M 1.59 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
6W9K 1.6 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
5UFS 2.12 Å, X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain…
7YXC 2.25 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
7YXD 2.3 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
7YXN 2.46 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
7YXR 2.5 Å, Crystal structure of mutant AncGR2-LBD (Y545A) bound to dexamethasone and SHP…
7YXO 2.99 Å, Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
7YXP 3.36 Å, Crystal structure of WT AncGR2-LBD WT bound to dexamethasone and SHP coregulator fragment

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