Research workbench
Prespliceosome structure provides insight into spliceosome assembly and regulation (MAP A2)
Analyse Prespliceosome structure provides insight into spliceosome assembly and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G90
- Type
- protein + RNA
- Length
- 7,484 residues
- Chains
- 38
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 SNRNA,U1 SNRNA,U1 SNRNA,U1 SNRNA,U1 snrna; U2 snrna; U1 small nuclear…
- UniProt
- P32605, Q00916, Q05900, P39682, Q03776, Q00539, Q03782, Q07508, P53207, P49955, Q04693, Q02554, Q99181, Q06835, P19736, Q07350, P32524, Q08963, P40567, P0C074, P40018, P43321, Q12330, P54999, P40204, Q02260, Q06217
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 37 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | U1 SNRNA,U1 SNRNA,U1 SNRNA,U1 SNRNA,U1 snrna | rna | 327 | — | — |
| 2 | U2 snrna | rna | 143 | — | — |
| A | U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein a | protein | 99 | 36% helix, 22% strand | P32605 |
| B | U1 small nuclear ribonucleoprotein 70 kda HOMOLOG,U1 small nuclear ribonucleoprotein 70 kda HOMOLOG,U1 small nuclear ribonucleoprotein 70 kda homolog | protein | 193 | 31% helix, 15% strand | Q00916 |
| C | U1 small nuclear ribonucleoprotein C | protein | 177 | 35% helix, 5% strand | Q05900 |
| D | Pre-mRNA-processing factor 39 | protein | 509 | 70% helix, 2% strand | P39682 |
| E | U1 small nuclear ribonucleoprotein component PRP42 | protein | 541 | 69% helix, 0% strand | Q03776 |
| F | Protein NAM8 | protein | 175 | 23% helix, 17% strand | Q00539 |
| G | 56 kda U1 small nuclear ribonucleoprotein component | protein | 216 | 49% helix, 16% strand | Q03782 |
| H | Protein LUC7,PROTEIN LUC7,PROTEIN LUC7 | protein | 158 | 64% helix, 3% strand | Q07508 |
| I | Yeast UBC4 pre-mRNA (mutant) | rna | 38 | — | — |
| J | U1 small nuclear ribonucleoprotein component SNU71 | protein | 42 | 29% helix, 19% strand | P53207 |
| O | U2 snrnp component HSH155 | protein | 833 | 78% helix, 0% strand | P49955 |
| P | Pre-mRNA-splicing factor RSE1 | protein | 1186 | 8% helix, 42% strand | Q04693 |
| Q | Cold sensitive U2 snrna suppressor 1 | protein | 220 | 35% helix, 5% strand | Q02554 |
| R | Protein HSH49 | protein | 173 | 29% helix, 33% strand | Q99181 |
| S | Pre-mRNA-splicing factor RDS3 | protein | 103 | 25% helix, 15% strand | Q06835 |
| T | Pre-mRNA-splicing factor PRP9 | protein | 462 | 58% helix, 3% strand | P19736 |
| U | Pre-mRNA-splicing factor PRP11,PRE-mRNA-splicing factor PRP11,PRE-mRNA-splicing factor PRP11 | protein | 196 | 17% helix, 22% strand | Q07350 |
| V | Pre-mRNA-splicing factor PRP21 | protein | 127 | 60% helix, 1% strand | P32524 |
| W | U2 small nuclear ribonucleoprotein a' | protein | 170 | 22% helix, 13% strand | Q08963 |
| X | Unknown | protein | 51 | 90% helix, 0% strand | — |
| Y | U2 small nuclear ribonucleoprotein B'' | protein | 84 | 26% helix, 23% strand | P40567 |
| Z | RDS3 complex subunit 10 | protein | 83 | 76% helix, 0% strand | P0C074 |
| b | Small nuclear ribonucleoprotein-associated protein B | protein | 121 | 26% helix, 28% strand | P40018 |
| d | Small nuclear ribonucleoprotein sm D3 | protein | 93 | 16% helix, 39% strand | P43321 |
| e | Small nuclear ribonucleoprotein E | protein | 77 | 13% helix, 48% strand | Q12330 |
| f, x | Small nuclear ribonucleoprotein F | protein | 73 | 11% helix, 48% strand | P54999 |
| g | Small nuclear ribonucleoprotein G | protein | 72 | 4% helix, 50% strand | P40204 |
| h | Small nuclear ribonucleoprotein sm D1 | protein | 107 | 28% helix, 33% strand | Q02260 |
| i | Small nuclear ribonucleoprotein sm D2 | protein | 99 | 18% helix, 43% strand | Q06217 |
| s | Small nuclear ribonucleoprotein-associated protein B | protein | 65 | 0% helix, 52% strand | P40018 |
| t | Small nuclear ribonucleoprotein sm D1 | protein | 72 | 13% helix, 54% strand | Q02260 |
| u | Small nuclear ribonucleoprotein sm D2 | protein | 92 | 22% helix, 49% strand | Q06217 |
| v | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 16% helix, 46% strand | P43321 |
| w | Small nuclear ribonucleoprotein E | protein | 77 | 14% helix, 48% strand | Q12330 |
| y | Small nuclear ribonucleoprotein G | protein | 75 | 8% helix, 52% strand | P40204 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains C, H, S, T, U
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 | 1142 | 0.88 | 0.90 | 121 | empty |
| 2 | 1019 | 0.87 | 0.88 | 108 | empty |
| 3 | 1180 | 0.84 | 0.85 | 88 | empty |
| 4 | 627 | 0.84 | 0.88 | 76 | empty |
| 5 | 843 | 0.83 | 0.85 | 66 | empty |
Interfaces
117 interfaces between chains.
- D–E · 3738 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 2848 Ų buried · 19 hydrogen bonds · protein-protein
- O–Q · 2780 Ų buried · 13 hydrogen bonds · protein-protein
- T–V · 2632 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 2194 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
- 6G90 · Prespliceosome structure provides insight into spliceosome assembly and regulation (map… · the same entry in another collection · chain H against H, 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 P32605
- Every structure of UniProt Q00916
- Every structure of UniProt Q05900
- Every structure of UniProt P39682
- Every structure of UniProt Q03776
- Every structure of UniProt Q00539
- Every structure of UniProt Q03782
- Every structure of UniProt Q07508
- Every structure of UniProt P53207
- Every structure of UniProt P49955
- Every structure of UniProt Q04693
- Every structure of UniProt Q02554
- Every structure of UniProt Q99181
- Every structure of UniProt Q06835
- Every structure of UniProt P19736
- Every structure of UniProt Q07350
- Every structure of UniProt P32524
- Every structure of UniProt Q08963
- Every structure of UniProt P40567
- Every structure of UniProt P0C074
- Every structure of UniProt P40018
- Every structure of UniProt P43321
- Every structure of UniProt Q12330
- Every structure of UniProt P54999
- Every structure of UniProt P40204
- Every structure of UniProt Q02260
- Every structure of UniProt Q06217
- Elsewhere: RCSB PDB 6G90 · PDBe 6G90 · UniProt P32605 · UniProt Q00916 · UniProt Q05900 · UniProt P39682 · UniProt Q03776 · UniProt Q00539 · UniProt Q03782 · UniProt Q07508 · UniProt P53207 · UniProt P49955 · UniProt Q04693 · UniProt Q02554 · UniProt Q99181 · UniProt Q06835 · UniProt P19736 · UniProt Q07350 · UniProt P32524 · UniProt Q08963 · UniProt P40567 · UniProt P0C074 · UniProt P40018 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217
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