Research workbench
Cryo-EM structure of 7SK core rnp with circular RNA
Analyse Cryo-EM structure of 7SK core rnp with circular RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SLQ
- Type
- protein + RNA
- Length
- 609 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7SK snrna methylphosphate capping enzyme; La-related protein 7; Minimal circular 7SK RNA
- EC
- 2.1.1.-
- UniProt
- Q7L2J0, Q4G0J3
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7SK snrna methylphosphate capping enzyme (EC 2.1.1.-) | protein | 237 | 32% helix, 17% strand | Q7L2J0 |
| B | La-related protein 7 | protein | 321 | 49% helix, 16% strand | Q4G0J3 |
| R | Minimal circular 7SK RNA | rna | 51 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.76 | 0.85 | 37 | SAH |
| 2 | 438 | 0.69 | 0.81 | 44 | empty |
| 3 | 56 | 0.68 | 0.96 | 13 | empty |
| 4 | 243 | 0.62 | 0.81 | 26 | empty |
| 5 | 323 | 0.56 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–R · 2541 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–B · 1380 Ų buried · 8 hydrogen bonds · protein-protein
- A–R · 936 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7SLQ · Cryo-EM structure of 7SK core RNP with circular RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q7L2J0 · AlphaFold monomer V2.0 prediction for 7SK snrna methylphosphate capping enzyme (Q7L2J0) · a predicted model of the same protein · chain A against A, TM-score 0.88
- Q4G0J3 · AlphaFold monomer V2.0 prediction for la-related protein 7 (Q4G0J3) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 Q7L2J0
- Every structure of UniProt Q4G0J3
- Elsewhere: RCSB PDB 7SLQ · PDBe 7SLQ · UniProt Q7L2J0 · UniProt Q4G0J3
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