Research workbench
Cryo-EM structure of rig-I:DSRNA filament in complex with riplet pryspry domain (trimer)
Analyse Cryo-EM structure of rig-I:DSRNA filament in complex with riplet pryspry domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JL3
- Type
- protein + RNA
- Length
- 2,541 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antiviral innate immune response receptor rig-I; E3 ubiquitin-protein ligase RNF135…
- EC
- 3.6.4.13, 2.3.2.27
- UniProt
- O95786, Q8IUD6
- Ligands
- ADP, ALF, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Antiviral innate immune response receptor rig-I (EC 3.6.4.13) | protein | 650 | 47% helix, 14% strand | O95786 |
| B, D, F | E3 ubiquitin-protein ligase RNF135 (EC 2.3.2.27) | protein | 169 | 0% helix, 43% strand | Q8IUD6 |
| X | Dsrna STRAND1 | rna | 42 | — | — |
| Y | Dsrna strand 2 | rna | 42 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, E
- ALF · Tetrafluoroaluminate ion · ligand · 3 copies · chains A, C, E
- MG · Magnesium ion · metal · 3 copies · chains A, C, E
- ZN · Zinc ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.83 | 0.84 | 103 | empty |
| 2 | 895 | 0.82 | 0.84 | 87 | empty |
| 3 | 1149 | 0.79 | 0.81 | 95 | empty |
| 4 | 737 | 0.73 | 0.79 | 80 | empty |
| 5 | 599 | 0.72 | 0.80 | 77 | ADP, ALF, MG |
Interfaces
14 interfaces between chains.
- X–Y · 1948 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- A–Y · 961 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–Y · 933 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–Y · 925 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–X · 888 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 7JL3 · Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer) · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q8IUD6 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF135 (Q8IUD6) · a predicted model of the same protein · chain B against A, TM-score 0.96
- O95786 · AlphaFold monomer V2.0 prediction for antiviral innate immune response receptor rig-I… · a predicted model of the same protein · chain E against A, TM-score 0.90
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 O95786
- Every structure of UniProt Q8IUD6
- Elsewhere: RCSB PDB 7JL3 · PDBe 7JL3 · UniProt O95786 · UniProt Q8IUD6
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