Research workbench
The cryo-EM structure of the palindromic DNA-bound usp-ecr nuclear receptor reveals an asymmetric organization with allosteric domain positioning
Analyse The cryo-EM structure of the palindromic DNA-bound usp-ecr nuclear receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UMM
- Type
- protein + DNA
- Length
- 682 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecr-usp; 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP *AP*CP*TP*TP*GP*TP)-3'…
- UniProt
- O18473, Q7SIF6
- Ligands
- EPH, P1A
- Pockets
- 11 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ecr-usp | protein | 78 | 38% helix, 8% strand | — |
| C | 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP *AP*CP*TP*TP*GP*TP)-3' | dna | 20 | — | — |
| D | 5'-D(*DGP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*DAP *AP*CP*CP*CP*TP*T)-3' | dna | 20 | — | — |
| E | Ecdysone receptor | protein | 87 | 39% helix, 9% strand | O18473 |
| F | Gene regulation protein | protein | 241 | 63% helix, 3% strand | Q7SIF6 |
| G | Ecdysone receptor | protein | 236 | 70% helix, 4% strand | O18473 |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains F
- P1A · 2,3,14,20,22-pentahydroxycholest-7-en-6-one · ligand · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.84 | 0.95 | 32 | P1A |
| 2 | 458 | 0.81 | 0.87 | 34 | EPH |
| 3 | 472 | 0.70 | 0.80 | 46 | empty |
| 4 | 666 | 0.69 | 0.78 | 68 | empty |
| 5 | 402 | 0.69 | 0.81 | 50 | empty |
Interfaces
9 interfaces between chains.
- F–G · 1364 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 852 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- C–E · 527 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–E · 510 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 489 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 4UMM · The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an… · the same entry in another collection · chain G against G, TM-score 1.00
- O18473 · AlphaFold monomer V2.0 prediction for ecdysone receptor (O18473) · a predicted model of the same protein · chain G against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O18473
- Every structure of UniProt Q7SIF6
- Elsewhere: RCSB PDB 4UMM · PDBe 4UMM · UniProt O18473 · UniProt Q7SIF6
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