MolNFT v1 · #127228 · protein + RNA
Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)
5MQF · Pre-mRNA-processing-splicing factor 8: “Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #127228 on GenesisL1: 3D structure…
- PDB
- 5MQF
- Type
- protein + RNA
- Length
- 11,894 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-processing-splicing factor 8; 116 kda U5 small nuclear ribonucleoprotein…
- EC
- 6.3.2.-, 5.2.1.8, 3.6.4.13
- UniProt
- Q6P2Q9, Q15029, Q13573, O43660, O60508, Q96DI7, Q9UMS4, O75934, Q99459, Q9HCS7, O95926, Q9BZJ0, Q9NW64, P41223, Q9P013, Q9UQ35, Q9HCG8, O60306, Q9Y3C6, P09661, P08579, P62316, P62306, P62304, P62308, P62318, P14678, P62314, Q9UNP9, P38919, Q14562
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 41 distinct chains · 29% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-processing-splicing factor 8 | protein | 1965 | 45% helix, 7% strand | Q6P2Q9 |
| B | 116 kda U5 small nuclear ribonucleoprotein component | protein | 902 | 33% helix, 19% strand | Q15029 |
| C | Snw domain-containing protein 1 | protein | 240 | 39% helix, 3% strand | Q13573 |
| D | Pleiotropic regulator 1 | protein | 315 | 0% helix, 36% strand | O43660 |
| E | Pre-mRNA-processing factor 17 | protein | 329 | 4% helix, 38% strand | O60508 |
| F | U5 small nuclear ribonucleoprotein 40 kda protein | protein | 307 | 0% helix, 45% strand | Q96DI7 |
| G | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 132 | 55% helix, 5% strand | Q9UMS4 |
| H, J | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 135 | 53% helix, 1% strand | Q9UMS4 |
| I | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 134 | 55% helix, 1% strand | Q9UMS4 |
| K | Pre-mRNA-splicing factor SPF27 | protein | 191 | 73% helix, 0% strand | O75934 |
| L | Cell division cycle 5-like protein | protein | 336 | 69% helix, 0% strand | Q99459 |
| M | Pre-mRNA-splicing factor SYF1 | protein | 706 | 61% helix, 0% strand | Q9HCS7 |
| N | Pre-mRNA-splicing factor SYF2 | protein | 115 | 40% helix, 0% strand | O95926 |
| O | Crooked neck-like protein 1 | protein | 564 | 65% helix, 0% strand | Q9BZJ0 |
| P | Pre-mRNA-splicing factor RBM22 | protein | 277 | 27% helix, 13% strand | Q9NW64 |
| Q | Protein BUD31 homolog | protein | 142 | 51% helix, 0% strand | P41223 |
| R | Spliceosome-associated protein CWC15 homolog | protein | 98 | 31% helix, 0% strand | Q9P013 |
| S | SERINE/ARGININE repetitive matrix protein 2 | protein | 30 | 17% helix, 0% strand | Q9UQ35 |
| T | Pre-mRNA-splicing factor CWC22 homolog | protein | 395 | 36% helix, 0% strand | Q9HCG8 |
| U | Intron-binding protein aquarius | protein | 1287 | 0% helix, 0% strand | O60306 |
| V | Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) | protein | 155 | 12% helix, 21% strand | Q9Y3C6 |
| W | U2 small nuclear ribonucleoprotein a' | protein | 162 | 27% helix, 17% strand | P09661 |
| X | U2 small nuclear ribonucleoprotein B'' | protein | 94 | 32% helix, 24% strand | P08579 |
| a | Small nuclear ribonucleoprotein sm D2 | protein | 99 | 19% helix, 44% strand | P62316 |
| b | Small nuclear ribonucleoprotein F | protein | 76 | 11% helix, 55% strand | P62306 |
| c, j | Small nuclear ribonucleoprotein E | protein | 79 | 14% helix, 43% strand | P62304 |
| d, k | Small nuclear ribonucleoprotein G | protein | 74 | 4% helix, 54% strand | P62308 |
| e | Small nuclear ribonucleoprotein sm D3 | protein | 84 | 13% helix, 45% strand | P62318 |
| f, m | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 71 | 7% helix, 54% strand | P14678 |
| g, n | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 16% helix, 45% strand | P62314 |
| h | Small nuclear ribonucleoprotein sm D2 | protein | 98 | 19% helix, 46% strand | P62316 |
| i | Small nuclear ribonucleoprotein F | protein | 74 | 15% helix, 57% strand | P62306 |
| l | Small nuclear ribonucleoprotein sm D3 | protein | 83 | 13% helix, 47% strand | P62318 |
| o | Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) | protein | 223 | 0% helix, 0% strand | Q9UNP9 |
| p | Eukaryotic initiation factor 4A-III (EC 3.6.4.13) | protein | 385 | 0% helix, 0% strand | P38919 |
| q | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 627 | 0% helix, 0% strand | Q14562 |
| Y | Minx pre-mRNA (intron) | rna | 32 | — | — |
| Z | Minx pre-mRNA (intron) | rna | 12 | — | — |
| 2 | Human gene for small nuclear RNA U2 (snrna U2) | rna | 140 | — | — |
| 5 | Homo sapiens U5 a small nuclear RNA | rna | 114 | — | — |
| 6 | Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA | rna | 89 | — | — |
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 | 986 | 0.83 | 0.85 | 98 | empty |
| 2 | 932 | 0.83 | 0.85 | 143 | empty |
| 3 | 1073 | 0.83 | 0.84 | 110 | empty |
| 4 | 1193 | 0.83 | 0.84 | 138 | empty |
| 5 | 746 | 0.83 | 0.87 | 111 | empty |
Interfaces
129 interfaces between chains.
- A–B · 1828 Ų buried · 3 hydrogen bonds · protein-protein
- A–5 · 1346 Ų buried · 15 hydrogen bonds · protein-nucleic
- 2–6 · 1264 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- A–C · 976 Ų buried · 1 hydrogen bond · protein-protein
- H–J · 933 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 5MQF · Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex) · the same entry in another collection · chain B against B, 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 Q13573
- Every structure of UniProt O43660
- Every structure of UniProt O60508
- Every structure of UniProt Q96DI7
- Every structure of UniProt Q9UMS4
- Every structure of UniProt O75934
- Every structure of UniProt Q99459
- Every structure of UniProt Q9HCS7
- Every structure of UniProt O95926
- Every structure of UniProt Q9BZJ0
- Every structure of UniProt Q9NW64
- Every structure of UniProt P41223
- Every structure of UniProt Q9P013
- Every structure of UniProt Q9UQ35
- Every structure of UniProt Q9HCG8
- Every structure of UniProt O60306
- Every structure of UniProt Q9Y3C6
- 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
- Every structure of UniProt Q9UNP9
- Every structure of UniProt P38919
- Every structure of UniProt Q14562
- Elsewhere: RCSB PDB 5MQF · PDBe 5MQF · UniProt Q6P2Q9 · UniProt Q15029 · UniProt Q13573 · UniProt O43660 · UniProt O60508 · UniProt Q96DI7 · UniProt Q9UMS4 · UniProt O75934 · UniProt Q99459 · UniProt Q9HCS7 · UniProt O95926 · UniProt Q9BZJ0 · UniProt Q9NW64 · UniProt P41223 · UniProt Q9P013 · UniProt Q9UQ35 · UniProt Q9HCG8 · UniProt O60306 · UniProt Q9Y3C6 · UniProt P09661 · UniProt P08579 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt Q9UNP9 · UniProt P38919 · UniProt Q14562
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