Research workbench
Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit
Analyse Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N8N
- Type
- protein + RNA
- Length
- 10,869 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c); Saccharomyces cerevisiae…
- Molecule
- Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA; 5S rRNA; 5.8S…
- EC
- 3.1.3.48, 3.6.1.-
- UniProt
- Q02256, Q12522, P53145, P38861, P0CX45, P14126, P10664, P26321, Q02326, P05737, P17076, P05738, P0C0W9, Q12690, P36105, P0CX27, P0CX25, P05748, P26784, P05740, P0CX49, P0CX82, P0CX23, Q02753, P05749, P0CX41, P04449, P04456, P05743, P0C2H6, P02406, P05747, P14120, P0C2H8, P38061, P05744, P87262, P0CX84, P05745, P49166, P49167, P04650, P0CH08
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.8 · 48 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA | rna | 3203 | — | — |
| B | 5S rRNA | rna | 121 | — | — |
| C | 5.8S rRNA | rna | 158 | — | — |
| Y | Tyrosine-protein phosphatase YVH1 (EC 3.1.3.48) | protein | 128 | 4% helix, 30% strand | Q02256 |
| X | Eukaryotic translation initiation factor 6 | protein | 234 | 26% helix, 23% strand | Q12522 |
| W | Large subunit GTPase 1 (EC 3.6.1.-) | protein | 377 | 37% helix, 8% strand | P53145 |
| V | 60S ribosomal export protein NMD3 | protein | 392 | 16% helix, 29% strand | P38861 |
| D | 60S ribosomal protein L2-A | protein | 246 | 6% helix, 27% strand | P0CX45 |
| E | 60S ribosomal protein L3 | protein | 384 | 13% helix, 28% strand | P14126 |
| F | 60S ribosomal protein L4-A | protein | 361 | 32% helix, 9% strand | P10664 |
| G | 60S ribosomal protein L5 | protein | 283 | 46% helix, 10% strand | P26321 |
| H | 60S ribosomal protein L6-A | protein | 155 | 22% helix, 17% strand | Q02326 |
| I | 60S ribosomal protein L7-A | protein | 220 | 51% helix, 13% strand | P05737 |
| J | 60S ribosomal protein L8-A | protein | 227 | 45% helix, 8% strand | P17076 |
| K | 60S ribosomal protein L9-A | protein | 188 | 19% helix, 40% strand | P05738 |
| M | 60S ribosomal protein L11-A | protein | 168 | 26% helix, 18% strand | P0C0W9 |
| N | 60S ribosomal protein L13-A | protein | 193 | 40% helix, 8% strand | Q12690 |
| O | 60S ribosomal protein L14-A | protein | 136 | 41% helix, 25% strand | P36105 |
| Q | 60S ribosomal protein L42-A | protein | 102 | 10% helix, 28% strand | P0CX27 |
| R | 60S ribosomal protein L43-A | protein | 88 | 40% helix, 15% strand | P0CX25 |
| S | Ribosomal Protein uL1 | protein | 210 | 26% helix, 3% strand | — |
| a | 60S ribosomal protein L15-A | protein | 203 | 35% helix, 17% strand | P05748 |
| b | 60S ribosomal protein L16-A | protein | 197 | 55% helix, 12% strand | P26784 |
| c | 60S ribosomal protein L17-A | protein | 183 | 37% helix, 22% strand | P05740 |
| d | 60S ribosomal protein L18-A | protein | 185 | 28% helix, 12% strand | P0CX49 |
| e | 60S ribosomal protein L19-A | protein | 151 | 63% helix, 3% strand | P0CX82 |
| f | 60S ribosomal protein L20-A | protein | 170 | 20% helix, 27% strand | P0CX23 |
| g | 60S ribosomal protein L21-A | protein | 159 | 16% helix, 23% strand | Q02753 |
| h | 60S ribosomal protein L22-A | protein | 97 | 32% helix, 29% strand | P05749 |
| i | 60S ribosomal protein L23-A | protein | 132 | 9% helix, 36% strand | P0CX41 |
| j | 60S ribosomal protein L24-A | protein | 61 | 25% helix, 21% strand | P04449 |
| k | 60S ribosomal protein L25 | protein | 121 | 26% helix, 21% strand | P04456 |
| l | 60S ribosomal protein L26-A | protein | 125 | 25% helix, 28% strand | P05743 |
| m | 60S ribosomal protein L27-A | protein | 135 | 21% helix, 24% strand | P0C2H6 |
| n | 60S ribosomal protein L28 | protein | 148 | 21% helix, 14% strand | P02406 |
| o | 60S ribosomal protein L29 | protein | 58 | 43% helix, 0% strand | P05747 |
| p | 60S ribosomal protein L30 | protein | 96 | 44% helix, 16% strand | P14120 |
| q | 60S ribosomal protein L31-A | protein | 107 | 32% helix, 25% strand | P0C2H8 |
| r | 60S ribosomal protein L32 | protein | 126 | 17% helix, 6% strand | P38061 |
| s | 60S ribosomal protein L33-A | protein | 106 | 4% helix, 46% strand | P05744 |
| t | 60S ribosomal protein L34-A | protein | 109 | 31% helix, 13% strand | P87262 |
| u | 60S ribosomal protein L35-A | protein | 119 | 59% helix, 3% strand | P0CX84 |
| v | 60S ribosomal protein L36-A | protein | 98 | 58% helix, 1% strand | P05745 |
| w | 60S ribosomal protein L37-A | protein | 84 | 19% helix, 7% strand | P49166 |
| x | 60S ribosomal protein L38 | protein | 77 | 21% helix, 38% strand | P49167 |
| y | 60S ribosomal protein L39 | protein | 50 | 32% helix, 0% strand | P04650 |
| z | Ubiquitin-60S ribosomal protein L40 | protein | 51 | 16% helix, 16% strand | P0CH08 |
| L | Ribosomal protein L12 | protein | 147 | 29% helix, 7% strand | — |
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 | 989 | 0.89 | 0.92 | 99 | empty |
| 2 | 715 | 0.89 | 0.93 | 96 | empty |
| 3 | 768 | 0.87 | 0.91 | 80 | empty |
| 4 | 637 | 0.87 | 0.92 | 78 | empty |
| 5 | 874 | 0.86 | 0.90 | 86 | empty |
Interfaces
145 interfaces between chains.
- A–E · 9160 Ų buried · 161 hydrogen bonds · protein-nucleic
- A–F · 8167 Ų buried · 135 hydrogen bonds · protein-nucleic
- A–a · 7547 Ų buried · 127 hydrogen bonds · protein-nucleic
- A–D · 7251 Ų buried · 159 hydrogen bonds · protein-nucleic
- A–C · 5211 Ų buried · 259 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- P0CX45 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-a (P0CX45) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P14126 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P14126) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P05748 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-a (P05748) · a predicted model of the same protein · chain a against A, TM-score 0.98
- P26321 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L5 (P26321) · a predicted model of the same protein · chain G against A, TM-score 0.97
- P0C0W9 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L11-a (P0C0W9) · a predicted model of the same protein · chain M against A, TM-score 0.97
- P0C2H6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L27-a (P0C2H6) · a predicted model of the same protein · chain m against A, TM-score 0.97
- P05743 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26-a (P05743) · a predicted model of the same protein · chain l against A, TM-score 0.97
- P26784 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L16-a (P26784) · a predicted model of the same protein · chain b against A, TM-score 0.97
- P14120 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P14120) · a predicted model of the same protein · chain p against A, TM-score 0.97
- P05738 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L9-a (P05738) · a predicted model of the same protein · chain K against A, TM-score 0.97
- P87262 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L34-a (P87262) · a predicted model of the same protein · chain t against A, TM-score 0.97
- P04449 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L24-a (P04449) · a predicted model of the same protein · chain j against A, TM-score 0.97
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 Q02256
- Every structure of UniProt Q12522
- Every structure of UniProt P53145
- Every structure of UniProt P38861
- Every structure of UniProt P0CX45
- Every structure of UniProt P14126
- Every structure of UniProt P10664
- Every structure of UniProt P26321
- Every structure of UniProt Q02326
- Every structure of UniProt P05737
- Every structure of UniProt P17076
- Every structure of UniProt P05738
- Every structure of UniProt P0C0W9
- Every structure of UniProt Q12690
- Every structure of UniProt P36105
- Every structure of UniProt P0CX27
- Every structure of UniProt P0CX25
- Every structure of UniProt P05748
- Every structure of UniProt P26784
- Every structure of UniProt P05740
- Every structure of UniProt P0CX49
- Every structure of UniProt P0CX82
- Every structure of UniProt P0CX23
- Every structure of UniProt Q02753
- Every structure of UniProt P05749
- Every structure of UniProt P0CX41
- Every structure of UniProt P04449
- Every structure of UniProt P04456
- Every structure of UniProt P05743
- Every structure of UniProt P0C2H6
- Every structure of UniProt P02406
- Every structure of UniProt P05747
- Every structure of UniProt P14120
- Every structure of UniProt P0C2H8
- Every structure of UniProt P38061
- Every structure of UniProt P05744
- Every structure of UniProt P87262
- Every structure of UniProt P0CX84
- Every structure of UniProt P05745
- Every structure of UniProt P49166
- Every structure of UniProt P49167
- Every structure of UniProt P04650
- Every structure of UniProt P0CH08
- Elsewhere: RCSB PDB 6N8N · PDBe 6N8N · UniProt Q02256 · UniProt Q12522 · UniProt P53145 · UniProt P38861 · UniProt P0CX45 · UniProt P14126 · UniProt P10664 · UniProt P26321 · UniProt Q02326 · UniProt P05737 · UniProt P17076 · UniProt P05738 · UniProt P0C0W9 · UniProt Q12690 · UniProt P36105 · UniProt P0CX27 · UniProt P0CX25 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P0CX82 · UniProt P0CX23 · UniProt Q02753 · UniProt P05749 · UniProt P0CX41 · UniProt P04449 · UniProt P04456 · UniProt P05743 · UniProt P0C2H6 · UniProt P02406 · UniProt P05747 · UniProt P14120 · UniProt P0C2H8 · UniProt P38061 · UniProt P05744 · UniProt P87262 · UniProt P0CX84 · UniProt P05745 · UniProt P49166 · UniProt P49167 · UniProt P04650 · UniProt P0CH08
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