Research workbench
Cryo-EM structure of the yeast spliceosome at 3.6 ångström resolution
Analyse Cryo-EM structure of the yeast spliceosome at 3.6 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JB9
- Type
- protein + RNA
- Length
- 10,837 residues
- Chains
- 43
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor SPP42; Pre-mRNA-splicing factor CWF10; U5 snrna; Small nuclear…
- EC
- 6.3.2.-, 5.2.1.8
- UniProt
- O14187, O94316, Q9UUC6, Q10163, O42661, O14036, Q9USZ3, O59734, O74966, O13615, O94620, Q09882, O14011, P39964, P87126, O59800, Q09909, P87051, O74772, O43071, P78794, Q9USV3, P87312, Q9P7R9, O94508, Q9USX8, Q7LL14
- Ligands
- GDP, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 39 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor SPP42 | protein | 1964 | 44% helix, 8% strand | O14187 |
| B | Pre-mRNA-splicing factor CWF10 | protein | 904 | 31% helix, 20% strand | O94316 |
| C | U5 snrna | rna | 105 | — | — |
| D | Small nuclear ribonucleoprotein sm D3 | protein | 96 | 16% helix, 41% strand | Q9UUC6 |
| E | Small nuclear ribonucleoprotein-associated protein B | protein | 98 | 5% helix, 37% strand | Q10163 |
| F, f | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 13% helix, 44% strand | O42661 |
| G | Small nuclear ribonucleoprotein sm D2 | protein | 95 | 19% helix, 37% strand | O14036 |
| H, m | Small nuclear ribonucleoprotein E | protein | 76 | 13% helix, 50% strand | Q9USZ3 |
| I, n | Small nuclear ribonucleoprotein F | protein | 73 | 11% helix, 56% strand | O59734 |
| J, o | Small nuclear ribonucleoprotein G | protein | 73 | 4% helix, 48% strand | O74966 |
| K | Pre-mRNA-splicing factor PRP5 | protein | 373 | 11% helix, 35% strand | O13615 |
| L | Pre-mRNA-splicing factor CWF17 | protein | 293 | 0% helix, 40% strand | O94620 |
| M | Pre-mRNA-processing protein 45 | protein | 207 | 32% helix, 6% strand | Q09882 |
| N | U6 snrna | rna | 90 | — | — |
| O | RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3') | rna | 8 | — | — |
| Q | RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3') | rna | 13 | — | — |
| P | U2 snrna | rna | 111 | — | — |
| S | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 132 | 55% helix, 8% strand | O14011 |
| T | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 134 | 55% helix, 9% strand | O14011 |
| U | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 430 | 19% helix, 37% strand | O14011 |
| V | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 131 | 55% helix, 8% strand | O14011 |
| W | Pre-mRNA-splicing factor CDC5 | protein | 426 | 78% helix, 0% strand | P39964 |
| Y | Pre-mRNA-splicing factor CWF2 | protein | 261 | 36% helix, 8% strand | P87126 |
| a | Pre-mRNA-splicing factor CWF5 | protein | 255 | 47% helix, 15% strand | O59800 |
| c | Pre-mRNA-splicing factor CWF19 | protein | 300 | 41% helix, 10% strand | Q09909 |
| d | Peptidyl-prolyl cis-trans isomerase PPI1 (EC 5.2.1.8) | protein | 155 | 14% helix, 28% strand | P87051 |
| e | Pre-mRNA-splicing factor CWF14 | protein | 144 | 45% helix, 0% strand | O74772 |
| g | Pre-mRNA-processing factor 17 | protein | 148 | 47% helix, 5% strand | O43071 |
| h | Pre-mRNA-splicing factor CWF15 | protein | 90 | 34% helix, 1% strand | P78794 |
| i | Pre-mRNA-splicing factor CWF7 | protein | 161 | 76% helix, 0% strand | Q9USV3 |
| R | Pre-mRNA-splicing factor CWF4 | protein | 575 | 73% helix, 0% strand | P87312 |
| r | Pre-mRNA-splicing factor CWF3 | protein | 573 | 80% helix, 0% strand | Q9P7R9 |
| X | Pre-mRNA-splicing factor CWF11 | protein | 1195 | 48% helix, 6% strand | O94508 |
| j | U2 small nuclear ribonucleoprotein a' | protein | 160 | 27% helix, 17% strand | Q9USX8 |
| k | Probable U2 small nuclear ribonucleoprotein B'' | protein | 89 | 34% helix, 25% strand | Q7LL14 |
| Z | Small nuclear ribonucleoprotein sm D3 | protein | 80 | 19% helix, 49% strand | Q9UUC6 |
| b | Small nuclear ribonucleoprotein-associated protein B | protein | 74 | 7% helix, 50% strand | Q10163 |
| l | Small nuclear ribonucleoprotein sm D2 | protein | 87 | 21% helix, 40% strand | O14036 |
| x | Unknown chain | protein | 272 | 90% helix, 0% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains X
- ZN · Zinc ion · metal · 7 copies · chains N, Y, a, c, e
- MG · Magnesium ion · metal · 4 copies · chains N
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 | 1088 | 0.87 | 0.88 | 103 | empty |
| 2 | 849 | 0.84 | 0.87 | 76 | empty |
| 3 | 489 | 0.84 | 0.91 | 54 | empty |
| 4 | 587 | 0.84 | 0.89 | 54 | empty |
| 5 | 934 | 0.84 | 0.85 | 81 | empty |
Interfaces
145 interfaces between chains.
- A–B · 6305 Ų buried · 48 hydrogen bonds · protein-protein
- A–c · 5014 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 3195 Ų buried · 66 hydrogen bonds · protein-nucleic
- W–i · 2767 Ų buried · 12 hydrogen bonds · protein-protein
- A–M · 2631 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3JB9 · Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution · the same entry in another collection · chain J against J, 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 O14187
- Every structure of UniProt O94316
- Every structure of UniProt Q9UUC6
- Every structure of UniProt Q10163
- Every structure of UniProt O42661
- Every structure of UniProt O14036
- Every structure of UniProt Q9USZ3
- Every structure of UniProt O59734
- Every structure of UniProt O74966
- Every structure of UniProt O13615
- Every structure of UniProt O94620
- Every structure of UniProt Q09882
- Every structure of UniProt O14011
- Every structure of UniProt P39964
- Every structure of UniProt P87126
- Every structure of UniProt O59800
- Every structure of UniProt Q09909
- Every structure of UniProt P87051
- Every structure of UniProt O74772
- Every structure of UniProt O43071
- Every structure of UniProt P78794
- Every structure of UniProt Q9USV3
- Every structure of UniProt P87312
- Every structure of UniProt Q9P7R9
- Every structure of UniProt O94508
- Every structure of UniProt Q9USX8
- Every structure of UniProt Q7LL14
- Elsewhere: RCSB PDB 3JB9 · PDBe 3JB9 · UniProt O14187 · UniProt O94316 · UniProt Q9UUC6 · UniProt Q10163 · UniProt O42661 · UniProt O14036 · UniProt Q9USZ3 · UniProt O59734 · UniProt O74966 · UniProt O13615 · UniProt O94620 · UniProt Q09882 · UniProt O14011 · UniProt P39964 · UniProt P87126 · UniProt O59800 · UniProt Q09909 · UniProt P87051 · UniProt O74772 · UniProt O43071 · UniProt P78794 · UniProt Q9USV3 · UniProt P87312 · UniProt Q9P7R9 · UniProt O94508 · UniProt Q9USX8 · UniProt Q7LL14
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