MolNFT v1 · #141369 · protein + RNA
Cryo-EM structure of a human activated spliceosome (early bact) at 4.9 ångström.
5Z58 · Pre-mRNA-processing-splicing factor 8: “Cryo-EM structure of a human activated spliceosome (early bact) at 4.9 ångström.”. Electron microscopy, 4 ligands (IHP, GTP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #141369 on…
- PDB
- 5Z58
- Type
- protein + RNA
- Length
- 13,305 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-processing-splicing factor 8; U5 snrna; 116 kda U5 small nuclear…
- EC
- 3.6.4.13, 5.2.1.8
- UniProt
- Q6P2Q9, Q15029, O75643, Q96DI7, P62318, P14678, P62314, P62316, P62306, P62304, P62308, P09661, P08579, Q12874, Q15459, Q15428, O75533, Q13435, Q15393, Q15427, Q9Y3B4, Q7RTV0, Q9BWJ5, Q9BZJ0, Q99459, O15541, Q9P013, O43660, Q9HCG8, Q8TAD8, Q9Y388, Q9BRD0, Q6UX04, O60231
- Ligands
- IHP, GTP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 43 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-processing-splicing factor 8 | protein | 2211 | 43% helix, 13% strand | Q6P2Q9 |
| B | U5 snrna | rna | 84 | — | — |
| C | 116 kda U5 small nuclear ribonucleoprotein component | protein | 860 | 38% helix, 23% strand | Q15029 |
| D | U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13) | protein | 1722 | 41% helix, 18% strand | O75643 |
| E | U5 small nuclear ribonucleoprotein 40 kda protein | protein | 299 | 0% helix, 49% strand | Q96DI7 |
| a | Small nuclear ribonucleoprotein sm D3 | protein | 81 | 14% helix, 48% strand | P62318 |
| b | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 82 | 4% helix, 49% strand | P14678 |
| c, j | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 16% helix, 45% strand | P62314 |
| d | Small nuclear ribonucleoprotein sm D2 | protein | 97 | 19% helix, 46% strand | P62316 |
| f, m | Small nuclear ribonucleoprotein F | protein | 74 | 15% helix, 57% strand | P62306 |
| e, l | Small nuclear ribonucleoprotein E | protein | 79 | 18% helix, 58% strand | P62304 |
| g | Small nuclear ribonucleoprotein G | protein | 74 | 8% helix, 54% strand | P62308 |
| F | U6 snrna | rna | 93 | — | — |
| G | Pre-mRNA | rna | 77 | — | — |
| H | U2 snrna | rna | 136 | — | — |
| h | Small nuclear ribonucleoprotein sm D3 | protein | 80 | 14% helix, 49% strand | P62318 |
| i | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 86 | 8% helix, 47% strand | P14678 |
| k | Small nuclear ribonucleoprotein sm D2 | protein | 85 | 21% helix, 51% strand | P62316 |
| n | Small nuclear ribonucleoprotein G | protein | 68 | 9% helix, 56% strand | P62308 |
| o | U2 small nuclear ribonucleoprotein a' | protein | 162 | 27% helix, 17% strand | P09661 |
| p | U2 small nuclear ribonucleoprotein B'' | protein | 165 | 30% helix, 25% strand | P08579 |
| w | Splicing factor 3A subunit 3 | protein | 437 | 59% helix, 3% strand | Q12874 |
| u | Splicing factor 3A subunit 1 | protein | 105 | 62% helix, 1% strand | Q15459 |
| v | Splicing factor 3A subunit 2 | protein | 98 | 5% helix, 22% strand | Q15428 |
| 1 | Splicing factor 3B subunit 1 | protein | 1038 | 71% helix, 0% strand | O75533 |
| 2 | Splicing factor 3B subunit 2 | protein | 183 | 34% helix, 3% strand | Q13435 |
| 3 | Splicing factor 3B subunit 3 | protein | 1177 | 7% helix, 45% strand | Q15393 |
| 4 | Splicing factor 3B subunit 4 | protein | 78 | 26% helix, 23% strand | Q15427 |
| 5 | Splicing factor 3B subunit 6 | protein | 108 | 27% helix, 22% strand | Q9Y3B4 |
| 6 | Phd finger-like domain-containing protein 5A | protein | 89 | 11% helix, 18% strand | Q7RTV0 |
| 7 | Splicing factor 3B subunit 5 | protein | 66 | 59% helix, 0% strand | Q9BWJ5 |
| J | Crooked neck-like protein 1 | protein | 522 | 73% helix, 0% strand | Q9BZJ0 |
| L | Cell division cycle 5-like protein | protein | 132 | 55% helix, 0% strand | Q99459 |
| M | Ring finger protein 113A | protein | 36 | 22% helix, 6% strand | O15541 |
| P | Spliceosome-associated protein CWC15 homolog | protein | 96 | 43% helix, 0% strand | Q9P013 |
| R | Skip | protein | 309 | 34% helix, 5% strand | — |
| T | Pleiotropic regulator 1 | protein | 313 | 0% helix, 48% strand | O43660 |
| V | Pre-mRNA-splicing factor CWC22 homolog | protein | 451 | 71% helix, 0% strand | Q9HCG8 |
| X | Smad nuclear-interacting protein 1 | protein | 158 | 9% helix, 31% strand | Q8TAD8 |
| Y | RNA-binding motif protein, X-linked 2 | protein | 104 | 32% helix, 25% strand | Q9Y388 |
| Z | BUD13 homolog | protein | 113 | 56% helix, 0% strand | Q9BRD0 |
| z | Peptidyl-prolyl cis-trans isomerase CWC27 homolog (EC 5.2.1.8) | protein | 177 | 12% helix, 28% strand | Q6UX04 |
| x | Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.4.13) | protein | 583 | 44% helix, 20% strand | O60231 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A, C
- MG · Magnesium ion · metal · 6 copies · chains C, F, G, A
- ZN · Zinc ion · metal · 4 copies · chains 6, G, M
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 | 1058 | 0.86 | 0.88 | 91 | empty |
| 2 | 930 | 0.85 | 0.87 | 130 | empty |
| 3 | 1045 | 0.85 | 0.86 | 97 | empty |
| 4 | 1025 | 0.85 | 0.86 | 111 | empty |
| 5 | 722 | 0.84 | 0.88 | 80 | empty |
Interfaces
127 interfaces between chains.
- A–C · 5775 Ų buried · 75 hydrogen bonds · protein-protein
- A–R · 5175 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2706 Ų buried · 41 hydrogen bonds · protein-nucleic
- 1–2 · 2640 Ų buried · 14 hydrogen bonds · protein-protein
- 3–7 · 2222 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5Z58 · Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom. · the same entry in another collection · chain f against f, 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 Q6P2Q9
- Every structure of UniProt Q15029
- Every structure of UniProt O75643
- Every structure of UniProt Q96DI7
- Every structure of UniProt P62318
- Every structure of UniProt P14678
- Every structure of UniProt P62314
- Every structure of UniProt P62316
- Every structure of UniProt P62306
- Every structure of UniProt P62304
- Every structure of UniProt P62308
- Every structure of UniProt P09661
- Every structure of UniProt P08579
- Every structure of UniProt Q12874
- Every structure of UniProt Q15459
- Every structure of UniProt Q15428
- Every structure of UniProt O75533
- Every structure of UniProt Q13435
- Every structure of UniProt Q15393
- Every structure of UniProt Q15427
- Every structure of UniProt Q9Y3B4
- Every structure of UniProt Q7RTV0
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt Q9BZJ0
- Every structure of UniProt Q99459
- Every structure of UniProt O15541
- Every structure of UniProt Q9P013
- Every structure of UniProt O43660
- Every structure of UniProt Q9HCG8
- Every structure of UniProt Q8TAD8
- Every structure of UniProt Q9Y388
- Every structure of UniProt Q9BRD0
- Every structure of UniProt Q6UX04
- Every structure of UniProt O60231
- Elsewhere: RCSB PDB 5Z58 · PDBe 5Z58 · UniProt Q6P2Q9 · UniProt Q15029 · UniProt O75643 · UniProt Q96DI7 · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P09661 · UniProt P08579 · UniProt Q12874 · UniProt Q15459 · UniProt Q15428 · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q15427 · UniProt Q9Y3B4 · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt Q9BZJ0 · UniProt Q99459 · UniProt O15541 · UniProt Q9P013 · UniProt O43660 · UniProt Q9HCG8 · UniProt Q8TAD8 · UniProt Q9Y388 · UniProt Q9BRD0 · UniProt Q6UX04 · UniProt O60231
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