Research workbench
Cryo-EM structure of a nucleolar pre-60S ribosome (RPF1-tap)
Analyse Cryo-EM structure of a nucleolar pre-60S ribosome (RPF1-tap) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z3G
- Type
- protein + RNA
- Length
- 7,901 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 25S rRNA; 5.8S rRNA; ITS2 RNA; Ribosome biogenesis protein RLP7; Ribosome biogenesis…
- EC
- 3.6.4.13
- UniProt
- P40693, P53927, P14126, P10664, P38779, Q02326, P05737, P17076, P05738, P53261, Q12522, P38805, Q12690, P36105, P05748, P26784, P05740, P0CX49, P53136, P0CX23, P35178, Q03532, P10962, Q08235, P36049, P05743, P38061, P05744, P0CX84, P05745, P49166
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 35 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 25S rRNA | rna | 1501 | — | — |
| B | 5.8S rRNA | rna | 156 | — | — |
| C | ITS2 RNA | rna | 65 | — | — |
| D | Ribosome biogenesis protein RLP7 | protein | 247 | 39% helix, 16% strand | P40693 |
| E | Ribosome biogenesis protein 15 | protein | 133 | 32% helix, 23% strand | P53927 |
| F | 60S ribosomal protein L3 | protein | 336 | 12% helix, 27% strand | P14126 |
| G | 60S ribosomal protein L4-a | protein | 361 | 27% helix, 7% strand | P10664 |
| H | Proteasome-interacting protein CIC1 | protein | 256 | 40% helix, 17% strand | P38779 |
| I | 60S ribosomal protein L6-a | protein | 150 | 19% helix, 15% strand | Q02326 |
| J | 60S ribosomal protein L7-a | protein | 239 | 54% helix, 10% strand | P05737 |
| K | 60S ribosomal protein L8-a | protein | 162 | 48% helix, 7% strand | P17076 |
| L | 60S ribosomal protein L9-a | protein | 191 | 17% helix, 35% strand | P05738 |
| M | Nucleolar protein 7 | protein | 371 | 42% helix, 6% strand | P53261 |
| N | Eukaryotic translation initiation factor 6 | protein | 226 | 21% helix, 18% strand | Q12522 |
| O | Ribosome production factor 1 | protein | 190 | 21% helix, 37% strand | P38805 |
| P | 60S ribosomal protein L13-a | protein | 108 | 40% helix, 8% strand | Q12690 |
| Q | 60S ribosomal protein L14-a | protein | 137 | 40% helix, 20% strand | P36105 |
| R | 60S ribosomal protein L15-a | protein | 175 | 34% helix, 18% strand | P05748 |
| S | 60S ribosomal protein L16-a | protein | 197 | 50% helix, 11% strand | P26784 |
| T | 60S ribosomal protein L17-a | protein | 136 | 35% helix, 25% strand | P05740 |
| U | 60S ribosomal protein L18-a | protein | 134 | 37% helix, 18% strand | P0CX49 |
| V | Ribosome biogenesis protein NSA1 | protein | 392 | 4% helix, 43% strand | P53136 |
| W | 60S ribosomal protein L20-a | protein | 170 | 21% helix, 25% strand | P0CX23 |
| X | Ribosomal RNA-processing protein 1 | protein | 202 | 75% helix, 0% strand | P35178 |
| Y | ATP-dependent RNA helicase HAS1 (EC 3.6.4.13) | protein | 438 | 38% helix, 11% strand | Q03532 |
| Z | Protein MAK16 | protein | 169 | 46% helix, 11% strand | P10962 |
| a | Ribosome biogenesis protein BRX1 | protein | 212 | 22% helix, 32% strand | Q08235 |
| b | RRNA-processing protein EBP2 | protein | 82 | 43% helix, 5% strand | P36049 |
| c | 60S ribosomal protein L26-a | protein | 125 | 26% helix, 26% strand | P05743 |
| d | Unassigned | protein | 154 | 69% helix, 0% strand | — |
| i | 60S ribosomal protein L32 | protein | 124 | 22% helix, 9% strand | P38061 |
| j | 60S ribosomal protein L33-a | protein | 106 | 7% helix, 41% strand | P05744 |
| l | 60S ribosomal protein L35-a | protein | 117 | 58% helix, 1% strand | P0CX84 |
| m | 60S ribosomal protein L36-a | protein | 67 | 75% helix, 0% strand | P05745 |
| n | 60S ribosomal protein L37-a | protein | 72 | 21% helix, 7% strand | P49166 |
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 | 961 | 0.87 | 0.89 | 97 | empty |
| 2 | 627 | 0.87 | 0.92 | 74 | empty |
| 3 | 1093 | 0.86 | 0.87 | 100 | empty |
| 4 | 1105 | 0.86 | 0.87 | 106 | empty |
| 5 | 615 | 0.86 | 0.91 | 69 | empty |
Interfaces
105 interfaces between chains.
- A–G · 7914 Ų buried · 164 hydrogen bonds · protein-nucleic
- A–F · 5433 Ų buried · 138 hydrogen bonds · protein-nucleic
- A–R · 4733 Ų buried · 77 hydrogen bonds · protein-nucleic
- A–B · 4037 Ų buried · 289 hydrogen bonds · nucleic-nucleic
- A–i · 3614 Ų buried · 59 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5Z3G · Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) · the same entry in another collection · chain K against K, 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 P40693
- Every structure of UniProt P53927
- Every structure of UniProt P14126
- Every structure of UniProt P10664
- Every structure of UniProt P38779
- Every structure of UniProt Q02326
- Every structure of UniProt P05737
- Every structure of UniProt P17076
- Every structure of UniProt P05738
- Every structure of UniProt P53261
- Every structure of UniProt Q12522
- Every structure of UniProt P38805
- Every structure of UniProt Q12690
- Every structure of UniProt P36105
- Every structure of UniProt P05748
- Every structure of UniProt P26784
- Every structure of UniProt P05740
- Every structure of UniProt P0CX49
- Every structure of UniProt P53136
- Every structure of UniProt P0CX23
- Every structure of UniProt P35178
- Every structure of UniProt Q03532
- Every structure of UniProt P10962
- Every structure of UniProt Q08235
- Every structure of UniProt P36049
- Every structure of UniProt P05743
- Every structure of UniProt P38061
- Every structure of UniProt P05744
- Every structure of UniProt P0CX84
- Every structure of UniProt P05745
- Every structure of UniProt P49166
- Elsewhere: RCSB PDB 5Z3G · PDBe 5Z3G · UniProt P40693 · UniProt P53927 · UniProt P14126 · UniProt P10664 · UniProt P38779 · UniProt Q02326 · UniProt P05737 · UniProt P17076 · UniProt P05738 · UniProt P53261 · UniProt Q12522 · UniProt P38805 · UniProt Q12690 · UniProt P36105 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P53136 · UniProt P0CX23 · UniProt P35178 · UniProt Q03532 · UniProt P10962 · UniProt Q08235 · UniProt P36049 · UniProt P05743 · UniProt P38061 · UniProt P05744 · UniProt P0CX84 · UniProt P05745 · UniProt P49166
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.