Research workbench
Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (without Rps2)
Analyse Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (without… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WTQ
- Type
- protein + RNA
- Length
- 4,334 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Saccharomyces cerevisiae
- Molecule
- 18S rRNA; 40S ribosomal protein S1-A; 40S ribosomal protein S4-A; 40S ribosomal protein…
- EC
- 2.1.1.309
- UniProt
- P33442, P0CX35, P0CX37, P26786, P0CX39, O13516, P0CX47, P05756, P06367, P0C0W1, P0CX29, P0CX31, P35997, P0CX33, Q99216, P25627, Q07381
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.7 · 18 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C2 | 18S rRNA | rna | 1255 | — | — |
| SB | 40S ribosomal protein S1-A | protein | 216 | 29% helix, 29% strand | P33442 |
| SE | 40S ribosomal protein S4-A | protein | 260 | 15% helix, 30% strand | P0CX35 |
| SG | 40S ribosomal protein S6-A | protein | 218 | 24% helix, 27% strand | P0CX37 |
| SH | 40S ribosomal protein S7-A | protein | 185 | 31% helix, 20% strand | P26786 |
| SI | 40S ribosomal protein S8-A | protein | 188 | 28% helix, 26% strand | P0CX39 |
| SJ | 40S ribosomal protein S9-A | protein | 185 | 52% helix, 5% strand | O13516 |
| SL | 40S ribosomal protein S11-A | protein | 146 | 3% helix, 36% strand | P0CX47 |
| SN | 40S ribosomal protein S13 | protein | 150 | 55% helix, 0% strand | P05756 |
| SO | 40S ribosomal protein S14-A | protein | 128 | 23% helix, 23% strand | P06367 |
| SW | 40S ribosomal protein S22-A | protein | 129 | 34% helix, 27% strand | P0C0W1 |
| SX | 40S ribosomal protein S23-A | protein | 144 | 22% helix, 21% strand | P0CX29 |
| SY | 40S ribosomal protein S24-A | protein | 134 | 37% helix, 27% strand | P0CX31 |
| Sb | 40S ribosomal protein S27-A | protein | 81 | 7% helix, 22% strand | P35997 |
| Se | 40S ribosomal protein S30-A | protein | 38 | 29% helix, 0% strand | P0CX33 |
| CA | Pre-rRNA-processing protein PNO1 | protein | 181 | 54% helix, 18% strand | Q99216 |
| CB | 18S rRNA (guanine(1575)-N(7))-methyltransferase (EC 2.1.1.309) | protein | 35 | 43% helix, 0% strand | P25627 |
| CC | Ribosome biogenesis protein TSR1 | protein | 661 | 25% helix, 28% strand | Q07381 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains Sb
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 | 689 | 0.86 | 0.90 | 66 | empty |
| 2 | 1086 | 0.86 | 0.87 | 77 | empty |
| 3 | 646 | 0.85 | 0.90 | 62 | empty |
| 4 | 692 | 0.85 | 0.89 | 77 | empty |
| 5 | 982 | 0.84 | 0.86 | 81 | empty |
Interfaces
42 interfaces between chains.
- C2–SG · 4919 Ų buried · 123 hydrogen bonds · protein-nucleic
- C2–SE · 4168 Ų buried · 60 hydrogen bonds · protein-nucleic
- C2–SI · 3914 Ų buried · 96 hydrogen bonds · protein-nucleic
- C2–SJ · 3629 Ų buried · 64 hydrogen bonds · protein-nucleic
- C2–SX · 3197 Ų buried · 48 hydrogen bonds · protein-nucleic
Compared structures
- P0C0W1 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22-a (P0C0W1) · a predicted model of the same protein · chain SW against A, TM-score 0.98
- P0CX39 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S8-a (P0CX39) · a predicted model of the same protein · chain SI against A, TM-score 0.98
- P05756 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S13 (P05756) · a predicted model of the same protein · chain SN against A, TM-score 0.97
- Q99216 · AlphaFold monomer V2.0 prediction for pre-rRNA-processing protein PNO1 (Q99216) · a predicted model of the same protein · chain CA against A, TM-score 0.97
- P06367 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14-a (P06367) · a predicted model of the same protein · chain SO against A, TM-score 0.95
- P0CX31 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S24-a (P0CX31) · a predicted model of the same protein · chain SY against A, TM-score 0.95
- P0CX47 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S11-a (P0CX47) · a predicted model of the same protein · chain SL against A, TM-score 0.94
- P35997 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S27-a (P35997) · a predicted model of the same protein · chain Sb against A, TM-score 0.92
- Q07381 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein TSR1 (Q07381) · a predicted model of the same protein · chain CC against A, TM-score 0.91
- P0CX29 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S23-a (P0CX29) · a predicted model of the same protein · chain SX against A, TM-score 0.86
- P25627 · AlphaFold monomer V2.0 prediction for 18S rRNA (GUANINE(1575)-N(7))-methyltransferase… · a predicted model of the same protein · chain CB against A, TM-score 0.72
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 P33442
- Every structure of UniProt P0CX35
- Every structure of UniProt P0CX37
- Every structure of UniProt P26786
- Every structure of UniProt P0CX39
- Every structure of UniProt O13516
- Every structure of UniProt P0CX47
- Every structure of UniProt P05756
- Every structure of UniProt P06367
- Every structure of UniProt P0C0W1
- Every structure of UniProt P0CX29
- Every structure of UniProt P0CX31
- Every structure of UniProt P35997
- Every structure of UniProt P0CX33
- Every structure of UniProt Q99216
- Every structure of UniProt P25627
- Every structure of UniProt Q07381
- Elsewhere: RCSB PDB 7WTQ · PDBe 7WTQ · UniProt P33442 · UniProt P0CX35 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P05756 · UniProt P06367 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt P35997 · UniProt P0CX33 · UniProt Q99216 · UniProt P25627 · UniProt Q07381
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