7YXO: WT AncGR2-LBD
Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment. Determined by X-ray diffraction at 2.99 Å resolution. Released 7 Dec 2022.
- Method
- X-ray diffraction
- Resolution
- 2.99 Å
- Organisms
- unidentified, Homo sapiens
- Chains
- 6
- Atoms
- 6,109
- Mol. weight
- 92.26 kDa
- Ligands
- DEX, CPS
- Released
- 7 Dec 2022
Explore 7YXO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7YXO contains 36 α-helices and 12 β-strands across 6 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: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 541-545 | 5 | |
| α-helix | 556-579 | 24 | |
| α-helix | 589-616 | 28 | |
| β-strand | 621-622 | 2 | 1 |
| β-strand | 628-629 | 2 | 1 |
| α-helix | 640-656 | 17 | |
| α-helix | 660-671 | 12 | |
| β-strand | 674-676 | 3 | 2 |
| α-helix | 683-702 | 20 | |
| α-helix | 714-741 | 28 | |
| α-helix | 743-745 | 3 | |
| α-helix | 751-766 | 16 | |
| β-strand | 769-771 | 3 | 2 |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-25 | 7 | |
Chain C: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 543-545 | 3 | |
| α-helix | 558-579 | 22 | |
| α-helix | 589-616 | 28 | |
| β-strand | 621-624 | 4 | 3 |
| β-strand | 627-629 | 3 | 3 |
| α-helix | 640-656 | 17 | |
| α-helix | 660-671 | 12 | |
| β-strand | 674-676 | 3 | 4 |
| α-helix | 683-702 | 20 | |
| α-helix | 711-741 | 31 | |
| α-helix | 743-745 | 3 | |
| α-helix | 751-766 | 16 | |
| β-strand | 769-771 | 3 | 4 |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-25 | 6 | |
Chain E: 13 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 532-539 | 8 | |
| α-helix | 543-545 | 3 | |
| α-helix | 556-579 | 24 | |
| α-helix | 589-616 | 28 | |
| β-strand | 621-622 | 2 | 5 |
| β-strand | 628-629 | 2 | 5 |
| α-helix | 632-634 | 3 | |
| α-helix | 640-656 | 17 | |
| α-helix | 660-671 | 12 | |
| β-strand | 675 | 1 | 6 |
| α-helix | 684-702 | 19 | |
| α-helix | 716-719 | 4 | |
| α-helix | 721-724 | 4 | |
| α-helix | 728-741 | 14 | |
| α-helix | 743-745 | 3 | |
| α-helix | 751-766 | 16 | |
| β-strand | 770 | 1 | 6 |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-24 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ancestral Glucocorticoid Receptor2 | A, C, E | protein | 248 | unidentified | A0A1X8XLE9 (AlphaFold model) |
| SHP NR Box 1 Peptide | B, D, F | protein | 11 | Homo sapiens | Q15466 (AlphaFold model) |
Sequence of entity 1 (A, C, E), FASTA
>7YXO_1 Ancestral Glucocorticoid Receptor2 (chains A, C, E)
FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLH
LDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLK
ISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNS
SQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGS
VKPLLFHQ
Sequence of entity 2 (B, D, F), FASTA
>7YXO_2 SHP NR Box 1 Peptide (chains B, D, F)
RPAILYALLSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| DEX | Dexamethasone | C22 H29 F O5 | 3 |
| CPS | 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate | C32 H58 N2 O7 S | 2 |
Water and common crystallization additives (SO4) are not listed.
Primary citation
The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Jimenez-Panizo, A., Alegre-Marti, A., Tettey, T.T. et al. Nucleic Acids Res (2022) 50:13063-13082. DOI 10.1093/nar/gkac1119 · PubMed
Other PDB entries of the same protein (UniProt A0A1X8XLE9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6W9L 1.45 Å, Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex…
- 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…
- 7YXP 3.36 Å, Crystal structure of WT AncGR2-LBD WT bound to dexamethasone and SHP coregulator fragment
Browse structure collections
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