Research workbench
Cryo-EM structure of the catalytic step I spliceosome (C complex) at 3.4 ångström resolution
Analyse Cryo-EM structure of the catalytic step I spliceosome (C complex) at 3.4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GMK
- Type
- protein + RNA
- Length
- 9,397 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor 8; Pre-mRNA-splicing factor SNU114; U5 snrna; U6 snrna; U2…
- EC
- 6.3.2.-
- UniProt
- P33334, P36048, Q03375, Q12417, P28004, P38241, Q12046, Q03772, P25337, P53333, Q03654, Q12309, P28320, P53854, P21374, P53277, Q04048, P40968, P32523, Q06091, P40018, Q12330, P54999, P40204, P43321, Q02260, Q06217, P40567, Q08963
- Ligands
- GTP, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 40 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor 8 | protein | 1910 | 46% helix, 10% strand | P33334 |
| C | Pre-mRNA-splicing factor SNU114 | protein | 878 | 35% helix, 21% strand | P36048 |
| D | U5 snrna | rna | 117 | — | — |
| E | U6 snrna | rna | 103 | — | — |
| L | U2 snrna | rna | 127 | — | — |
| M | INTRON_BPS | rna | 29 | — | — |
| B | 5'-exon | rna | 13 | — | — |
| N | 5'-splicing site | rna | 15 | — | — |
| J | Pre-mRNA-splicing factor CWC21 | protein | 27 | 0% helix, 11% strand | Q03375 |
| O | Pre-mRNA-splicing factor PRP46 | protein | 337 | 3% helix, 40% strand | Q12417 |
| P | Pre-mRNA-processing protein 45 | protein | 201 | 43% helix, 1% strand | P28004 |
| Q | Pre-mRNA-splicing factor SLT11 | protein | 185 | 23% helix, 12% strand | P38241 |
| R | Pre-mRNA-splicing factor CWC2 | protein | 261 | 36% helix, 13% strand | Q12046 |
| S | Pre-mRNA-splicing factor CWC15 | protein | 69 | 26% helix, 0% strand | Q03772 |
| T | Pre-mRNA-splicing factor BUD31 | protein | 157 | 50% helix, 0% strand | P25337 |
| Z | Pre-mRNA-splicing factor CWC22 | protein | 447 | 67% helix, 0% strand | P53333 |
| c | Pre-mRNA-splicing factor CEF1 | protein | 436 | 72% helix, 0% strand | Q03654 |
| d | Pre-mRNA-splicing factor CLF1 | protein | 549 | 75% helix, 0% strand | Q12309 |
| F | Protein CWC16 | protein | 115 | 12% helix, 27% strand | P28320 |
| G | Pre-mRNA-splicing factor CWC25 | protein | 41 | 66% helix, 0% strand | P53854 |
| H | Pre-mRNA-splicing factor ISY1 | protein | 95 | 64% helix, 1% strand | P21374 |
| I | Pre-mRNA-splicing factor SYF2 | protein | 102 | 67% helix, 4% strand | P53277 |
| v | Pre-mRNA-splicing factor SYF1 | protein | 673 | 81% helix, 0% strand | Q04048 |
| n | Pre-mRNA-processing factor 17 | protein | 299 | 4% helix, 41% strand | P40968 |
| o | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 126 | 57% helix, 6% strand | P32523 |
| p | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 128 | 54% helix, 7% strand | P32523 |
| q | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 387 | 20% helix, 36% strand | P32523 |
| r | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 125 | 55% helix, 8% strand | P32523 |
| t | Pre-mRNA-splicing factor SNT309 | protein | 156 | 76% helix, 0% strand | Q06091 |
| k | Small nuclear ribonucleoprotein-associated protein B | protein | 80 | 4% helix, 50% strand | P40018 |
| i, u | Small nuclear ribonucleoprotein E | protein | 75 | 19% helix, 41% strand | Q12330 |
| h, w | Small nuclear ribonucleoprotein F | protein | 70 | 14% helix, 56% strand | P54999 |
| j, x | Small nuclear ribonucleoprotein G | protein | 69 | 0% helix, 46% strand | P40204 |
| l, y | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 20% helix, 45% strand | P43321 |
| m, z | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 15% helix, 46% strand | Q02260 |
| g | Small nuclear ribonucleoprotein sm D2 | protein | 94 | 23% helix, 40% strand | Q06217 |
| s | Small nuclear ribonucleoprotein-associated protein B | protein | 78 | 4% helix, 51% strand | P40018 |
| e | Small nuclear ribonucleoprotein sm D2 | protein | 65 | 0% helix, 55% strand | Q06217 |
| a | U2 small nuclear ribonucleoprotein B'' | protein | 81 | 28% helix, 19% strand | P40567 |
| b | U2 small nuclear ribonucleoprotein a' | protein | 135 | 22% helix, 20% strand | Q08963 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, C
- ZN · Zinc ion · metal · 7 copies · chains Q, E, R, T, F
- MG · Magnesium ion · metal · 6 copies · chains C, E, B, N, A
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 | 1006 | 0.89 | 0.91 | 114 | MG |
| 2 | 861 | 0.88 | 0.91 | 96 | MG |
| 3 | 972 | 0.87 | 0.88 | 88 | empty |
| 4 | 617 | 0.86 | 0.91 | 79 | empty |
| 5 | 1091 | 0.86 | 0.87 | 78 | empty |
Interfaces
158 interfaces between chains.
- A–C · 4908 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 3600 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–P · 2386 Ų buried · 13 hydrogen bonds · protein-protein
- A–Z · 2108 Ų buried · 28 hydrogen bonds · protein-protein
- A–S · 2098 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5GMK · Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom… · the same entry in another collection · chain P against P, 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 P33334
- Every structure of UniProt P36048
- Every structure of UniProt Q03375
- Every structure of UniProt Q12417
- Every structure of UniProt P28004
- Every structure of UniProt P38241
- Every structure of UniProt Q12046
- Every structure of UniProt Q03772
- Every structure of UniProt P25337
- Every structure of UniProt P53333
- Every structure of UniProt Q03654
- Every structure of UniProt Q12309
- Every structure of UniProt P28320
- Every structure of UniProt P53854
- Every structure of UniProt P21374
- Every structure of UniProt P53277
- Every structure of UniProt Q04048
- Every structure of UniProt P40968
- Every structure of UniProt P32523
- Every structure of UniProt Q06091
- Every structure of UniProt P40018
- Every structure of UniProt Q12330
- Every structure of UniProt P54999
- Every structure of UniProt P40204
- Every structure of UniProt P43321
- Every structure of UniProt Q02260
- Every structure of UniProt Q06217
- Every structure of UniProt P40567
- Every structure of UniProt Q08963
- Elsewhere: RCSB PDB 5GMK · PDBe 5GMK · UniProt P33334 · UniProt P36048 · UniProt Q03375 · UniProt Q12417 · UniProt P28004 · UniProt P38241 · UniProt Q12046 · UniProt Q03772 · UniProt P25337 · UniProt P53333 · UniProt Q03654 · UniProt Q12309 · UniProt P28320 · UniProt P53854 · UniProt P21374 · UniProt P53277 · UniProt Q04048 · UniProt P40968 · UniProt P32523 · UniProt Q06091 · UniProt P40018 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt P43321 · UniProt Q02260 · UniProt Q06217 · UniProt P40567 · UniProt Q08963
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