Research workbench
The cryo-EM structure of the human 17S U2 snrnp
Analyse The cryo-EM structure of the human 17S U2 snrnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EVO
- Type
- protein + RNA
- Length
- 4,817 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U2 snrna; Splicing factor 3B subunit 1; Splicing factor 3B subunit 2; Splicing factor 3B…
- EC
- 3.6.4.13
- UniProt
- O75533, Q13435, Q15393, Q15427, Q9BWJ5, Q7RTV0, Q15459, Q15428, Q12874, O43719, A0A0C4DG89, P09661, P08579, P62316, P62306, P62304, P62308, P62318, P14678, P62314
- Ligands
- 9B0, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 21 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | U2 snrna | rna | 148 | — | — |
| 1 | Splicing factor 3B subunit 1 | protein | 815 | 76% helix, 0% strand | O75533 |
| 2 | Splicing factor 3B subunit 2 | protein | 182 | 27% helix, 5% strand | Q13435 |
| 3 | Splicing factor 3B subunit 3 | protein | 1180 | 7% helix, 46% strand | Q15393 |
| 4 | Splicing factor 3B subunit 4 | protein | 160 | 23% helix, 29% strand | Q15427 |
| 5 | Splicing factor 3B subunit 5 | protein | 66 | 61% helix, 0% strand | Q9BWJ5 |
| 6 | Phd finger-like domain-containing protein 5A | protein | 85 | 13% helix, 25% strand | Q7RTV0 |
| A | Splicing factor 3A subunit 1 | protein | 123 | 59% helix, 0% strand | Q15459 |
| B | Splicing factor 3A subunit 2 | protein | 100 | 4% helix, 33% strand | Q15428 |
| C | Splicing factor 3A subunit 3 | protein | 422 | 55% helix, 3% strand | Q12874 |
| D | HIV tat-specific factor 1 | protein | 200 | 28% helix, 26% strand | O43719 |
| E | RNA helicase (EC 3.6.4.13) | protein | 455 | 43% helix, 13% strand | A0A0C4DG89 |
| F | U2 small nuclear ribonucleoprotein a' | protein | 162 | 23% helix, 17% strand | P09661 |
| G | U2 small nuclear ribonucleoprotein B'' | protein | 166 | 28% helix, 27% strand | P08579 |
| a | Small nuclear ribonucleoprotein sm D2 | protein | 90 | 18% helix, 49% strand | P62316 |
| b | Small nuclear ribonucleoprotein F | protein | 74 | 9% helix, 58% strand | P62306 |
| c | Small nuclear ribonucleoprotein E | protein | 79 | 14% helix, 53% strand | P62304 |
| d | Small nuclear ribonucleoprotein G | protein | 74 | 0% helix, 50% strand | P62308 |
| e | Small nuclear ribonucleoprotein sm D3 | protein | 83 | 10% helix, 43% strand | P62318 |
| f | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 71 | 4% helix, 52% strand | P14678 |
| g | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 12% helix, 46% strand | P62314 |
Ligands and binding sites
- 9B0 · [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R}, 3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate · ligand · chains 1, 6
- ZN · Zinc ion · metal · 4 copies · chains 6, C
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 | 1067 | 0.84 | 0.85 | 101 | empty |
| 2 | 1154 | 0.84 | 0.85 | 78 | empty |
| 3 | 681 | 0.79 | 0.84 | 89 | empty |
| 4 | 1077 | 0.78 | 0.80 | 69 | empty |
| 5 | 275 | 0.77 | 0.90 | 55 | empty |
Interfaces
39 interfaces between chains.
- 3–5 · 2333 Ų buried · 26 hydrogen bonds · protein-protein
- 1–2 · 2284 Ų buried · 14 hydrogen bonds · protein-protein
- 1–3 · 2178 Ų buried · 20 hydrogen bonds · protein-protein
- 1–E · 1910 Ų buried · 16 hydrogen bonds · protein-protein
- 1–5 · 1454 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7EVO · The cryo-EM structure of the human 17S U2 snRNP · the same entry in another collection · chain D against D, TM-score 1.00
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 O75533
- Every structure of UniProt Q13435
- Every structure of UniProt Q15393
- Every structure of UniProt Q15427
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt Q7RTV0
- Every structure of UniProt Q15459
- Every structure of UniProt Q15428
- Every structure of UniProt Q12874
- Every structure of UniProt O43719
- Every structure of UniProt A0A0C4DG89
- Every structure of UniProt P09661
- Every structure of UniProt P08579
- Every structure of UniProt P62316
- Every structure of UniProt P62306
- Every structure of UniProt P62304
- Every structure of UniProt P62308
- Every structure of UniProt P62318
- Every structure of UniProt P14678
- Every structure of UniProt P62314
- Elsewhere: RCSB PDB 7EVO · PDBe 7EVO · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q15427 · UniProt Q9BWJ5 · UniProt Q7RTV0 · UniProt Q15459 · UniProt Q15428 · UniProt Q12874 · UniProt O43719 · UniProt A0A0C4DG89 · UniProt P09661 · UniProt P08579 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P62318 · UniProt P14678 · UniProt P62314
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