MolNFT v1 · #153205 · protein + RNA
Cryo-EM structure of the yeast B*-B1 complex at an average resolution of 3.86 ångström
6J6N · Pre-mRNA-splicing factor 8: “Cryo-EM structure of the yeast B*-B1 complex at an average resolution of 3.86 ångström”. Electron microscopy, 4 ligands (IHP, GTP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #153205 on…
- PDB
- 6J6N
- Type
- protein + RNA
- Length
- 9,526 residues
- Chains
- 41
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor 8; Pre-mRNA-splicing factor SNU114; Pre-mRNA-splicing factor…
- EC
- 2.3.2.27
- UniProt
- P33334, P36048, Q03375, Q12417, P28004, P38241, Q12046, Q03772, P25337, P53333, Q03654, Q12309, P53277, P40968, P21374, Q04048, P40567, Q08963, Q06091, Q12330, Q02260, P40204, P54999, Q06217, P40018, P43321, P32523
- Ligands
- IHP, GTP, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 37 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor 8 | protein | 1913 | 44% helix, 10% strand | P33334 |
| C | Pre-mRNA-splicing factor SNU114 | protein | 920 | 35% helix, 23% strand | P36048 |
| J | Pre-mRNA-splicing factor CWC21 | protein | 27 | 0% helix, 11% strand | Q03375 |
| O | Pre-mRNA-splicing factor PRP46 | protein | 357 | 3% helix, 45% strand | Q12417 |
| P | Pre-mRNA-processing protein 45 | protein | 205 | 37% helix, 3% strand | P28004 |
| Q | Pre-mRNA-splicing factor SLT11 | protein | 292 | 34% helix, 16% strand | P38241 |
| R | Pre-mRNA-splicing factor CWC2 | protein | 261 | 31% helix, 13% strand | Q12046 |
| S | Pre-mRNA-splicing factor CWC15 | protein | 70 | 24% helix, 0% strand | Q03772 |
| T | Pre-mRNA-splicing factor BUD31 | protein | 157 | 51% helix, 0% strand | P25337 |
| Z | Pre-mRNA-splicing factor CWC22 | protein | 447 | 68% helix, 0% strand | P53333 |
| c | Pre-mRNA-splicing factor CEF1 | protein | 436 | 70% helix, 0% strand | Q03654 |
| d | Pre-mRNA-splicing factor CLF1 | protein | 566 | 80% helix, 0% strand | Q12309 |
| I | Pre-mRNA-splicing factor SYF2 | protein | 102 | 64% helix, 4% strand | P53277 |
| n | Pre-mRNA-processing factor 17 | protein | 299 | 3% helix, 44% strand | P40968 |
| H | Pre-mRNA-splicing factor ISY1 | protein | 71 | 62% helix, 0% strand | P21374 |
| B | UBC4 pre-mRNA | rna | 57 | — | — |
| D | U5 snrna | rna | 179 | — | — |
| E | U6 snrna | rna | 103 | — | — |
| L | U2 snrna | rna | 205 | — | — |
| v | Pre-mRNA-splicing factor SYF1 | protein | 722 | 74% helix, 0% strand | Q04048 |
| a | U2 small nuclear ribonucleoprotein B'' | protein | 84 | 26% helix, 24% strand | P40567 |
| b | U2 small nuclear ribonucleoprotein a' | protein | 169 | 22% helix, 12% strand | Q08963 |
| t | Pre-mRNA-splicing factor SNT309 | protein | 156 | 77% helix, 0% strand | Q06091 |
| u, i | Small nuclear ribonucleoprotein E | protein | 74 | 18% helix, 51% strand | Q12330 |
| m | Small nuclear ribonucleoprotein sm D1 | protein | 119 | 24% helix, 30% strand | Q02260 |
| j, x | Small nuclear ribonucleoprotein G | protein | 75 | 4% helix, 49% strand | P40204 |
| h, w | Small nuclear ribonucleoprotein F | protein | 68 | 10% helix, 51% strand | P54999 |
| g, e | Small nuclear ribonucleoprotein sm D2 | protein | 101 | 22% helix, 46% strand | Q06217 |
| k | Small nuclear ribonucleoprotein-associated protein B | protein | 100 | 8% helix, 37% strand | P40018 |
| s | Small nuclear ribonucleoprotein-associated protein B | protein | 93 | 8% helix, 38% strand | P40018 |
| l | Small nuclear ribonucleoprotein sm D3 | protein | 83 | 24% helix, 43% strand | P43321 |
| y | Small nuclear ribonucleoprotein sm D3 | protein | 81 | 23% helix, 47% strand | P43321 |
| z | Small nuclear ribonucleoprotein sm D1 | protein | 108 | 20% helix, 34% strand | Q02260 |
| r | Pre-mRNA-processing factor 19 (EC 2.3.2.27) | protein | 125 | 55% helix, 10% strand | P32523 |
| p | Pre-mRNA-processing factor 19 (EC 2.3.2.27) | protein | 128 | 55% helix, 7% strand | P32523 |
| q | Pre-mRNA-processing factor 19 (EC 2.3.2.27) | protein | 129 | 58% helix, 7% strand | P32523 |
| o | Pre-mRNA-processing factor 19 (EC 2.3.2.27) | protein | 126 | 57% helix, 7% strand | P32523 |
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, E
- ZN · Zinc ion · metal · 6 copies · chains Q, R, T
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 | 857 | 0.88 | 0.91 | 105 | empty |
| 2 | 1035 | 0.88 | 0.89 | 81 | MG |
| 3 | 924 | 0.87 | 0.88 | 78 | empty |
| 4 | 873 | 0.86 | 0.88 | 94 | empty |
| 5 | 618 | 0.86 | 0.90 | 78 | empty |
Interfaces
139 interfaces between chains.
- A–C · 5268 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 3730 Ų buried · 73 hydrogen bonds · protein-nucleic
- Q–R · 2432 Ų buried · 13 hydrogen bonds · protein-protein
- A–P · 2381 Ų buried · 17 hydrogen bonds · protein-protein
- A–Z · 2275 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6J6N · Cryo-EM structure of the yeast B*-b1 complex at an average resolution of 3.86 angstrom · the same entry in another collection · chain c against c, 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 P53277
- Every structure of UniProt P40968
- Every structure of UniProt P21374
- Every structure of UniProt Q04048
- Every structure of UniProt P40567
- Every structure of UniProt Q08963
- Every structure of UniProt Q06091
- Every structure of UniProt Q12330
- Every structure of UniProt Q02260
- Every structure of UniProt P40204
- Every structure of UniProt P54999
- Every structure of UniProt Q06217
- Every structure of UniProt P40018
- Every structure of UniProt P43321
- Every structure of UniProt P32523
- Elsewhere: RCSB PDB 6J6N · PDBe 6J6N · 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 P53277 · UniProt P40968 · UniProt P21374 · UniProt Q04048 · UniProt P40567 · UniProt Q08963 · UniProt Q06091 · UniProt Q12330 · UniProt Q02260 · UniProt P40204 · UniProt P54999 · UniProt Q06217 · UniProt P40018 · UniProt P43321 · UniProt P32523
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