Research workbench
State B architectural model (NSA1-tap flag-YTM1) - visualizing the assembly pathway of nucleolar pre-60S ribosomes
Analyse State B architectural model (NSA1-tap flag-YTM1) - visualizing the assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EM4
- Type
- protein + RNA
- Length
- 7,792 residues
- Chains
- 37
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome production factor 1; 60S ribosomal protein L7-a; Protein MAK16; Ribosomal…
- EC
- 3.6.4.13
- UniProt
- P38805, P05737, P10962, P35178, P53136, Q08235, P36049, Q07915, P40007, Q12522, P14126, P10664, P38061, Q02326, P05744, P17076, P0CX84, O14455, P49166, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX23, P0CX41, P05743, Q03532, P38779, P53261, P53927, P40693, Q04660
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 37 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| x | Ribosome production factor 1 | protein | 267 | 31% helix, 22% strand | P38805 |
| F | 60S ribosomal protein L7-a | protein | 241 | 54% helix, 13% strand | P05737 |
| 3 | Protein MAK16 | protein | 173 | 40% helix, 15% strand | P10962 |
| 4 | Ribosomal RNA-processing protein 1 | protein | 220 | 58% helix, 0% strand | P35178 |
| 5 | Ribosome biogenesis protein NSA1 | protein | 385 | 3% helix, 46% strand | P53136 |
| A | Ribosome biogenesis protein BRX1 | protein | 145 | 23% helix, 23% strand | Q08235 |
| J | RRNA-processing protein EBP2 | protein | 66 | 50% helix, 2% strand | P36049 |
| u | Ribosome biogenesis protein RLP24 | protein | 116 | 39% helix, 9% strand | Q07915 |
| v | Nucleolar protein 16 | protein | 130 | 48% helix, 0% strand | P40007 |
| y | Eukaryotic translation initiation factor 6 | protein | 225 | 27% helix, 23% strand | Q12522 |
| B | 60S ribosomal protein L3 | protein | 333 | 14% helix, 30% strand | P14126 |
| C | 60S ribosomal protein L4-a | protein | 343 | 29% helix, 10% strand | P10664 |
| e | 60S ribosomal protein L32 | protein | 125 | 19% helix, 11% strand | P38061 |
| E | 60S ribosomal protein L6-a | protein | 151 | 23% helix, 20% strand | Q02326 |
| f | 60S ribosomal protein L33-a | protein | 106 | 7% helix, 45% strand | P05744 |
| G | 60S ribosomal protein L8-a | protein | 159 | 45% helix, 9% strand | P17076 |
| h | 60S ribosomal protein L35-a | protein | 119 | 55% helix, 3% strand | P0CX84 |
| i | 60S ribosomal protein L36-B | protein | 74 | 78% helix, 0% strand | O14455 |
| j | 60S ribosomal protein L37-a | protein | 71 | 23% helix, 8% strand | P49166 |
| L | 60S ribosomal protein L13-a | protein | 108 | 44% helix, 13% strand | Q12690 |
| M | 60S ribosomal protein L14-a | protein | 134 | 38% helix, 25% strand | P36105 |
| N | 60S ribosomal protein L15-a | protein | 177 | 39% helix, 19% strand | P05748 |
| O | 60S ribosomal protein L16-a | protein | 197 | 51% helix, 5% strand | P26784 |
| P | 60S ribosomal protein L17-a | protein | 137 | 36% helix, 26% strand | P05740 |
| Q | 60S ribosomal protein L18-a | protein | 131 | 38% helix, 18% strand | P0CX49 |
| S | 60S ribosomal protein L20-a | protein | 170 | 21% helix, 29% strand | P0CX23 |
| V | 60S ribosomal protein L23-a | protein | 126 | 9% helix, 39% strand | P0CX41 |
| Y | 60S ribosomal protein L26-a | protein | 125 | 26% helix, 32% strand | P05743 |
| 1 | 25S ribosomal RNA | rna | 1556 | — | — |
| 2 | 5.8S ribosomal RNA | rna | 158 | — | — |
| D | ATP-dependent RNA helicase HAS1 (EC 3.6.4.13) | protein | 194 | 35% helix, 12% strand | Q03532 |
| K | Proteasome-interacting protein CIC1 | protein | 246 | 38% helix, 19% strand | P38779 |
| n | Pescadillo homolog | protein | 312 | 45% helix, 6% strand | P53261 |
| o | Ribosome biogenesis protein 15 | protein | 116 | 33% helix, 24% strand | P53927 |
| t | Ribosome biogenesis protein RLP7 | protein | 248 | 38% helix, 13% strand | P40693 |
| 6 | Internal transcribed spacer 1 | rna | 65 | — | — |
| H | Ribosome biogenesis protein ERB1 | protein | 143 | 37% helix, 0% strand | Q04660 |
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 | 731 | 0.77 | 0.82 | 83 | empty |
| 2 | 591 | 0.76 | 0.83 | 81 | empty |
| 3 | 839 | 0.74 | 0.79 | 156 | empty |
| 4 | 1133 | 0.73 | 0.78 | 123 | empty |
| 5 | 738 | 0.73 | 0.80 | 102 | empty |
Interfaces
102 interfaces between chains.
- C–1 · 2865 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–1 · 1705 Ų buried · 37 hydrogen bonds · protein-nucleic
- N–1 · 1501 Ų buried · 12 hydrogen bonds · protein-nucleic
- e–1 · 1490 Ų buried · 18 hydrogen bonds · protein-nucleic
- 1–2 · 1266 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Compared structures
- 6EM4 · State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of… · the same entry in another collection · chain B against B, 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 P38805
- Every structure of UniProt P05737
- Every structure of UniProt P10962
- Every structure of UniProt P35178
- Every structure of UniProt P53136
- Every structure of UniProt Q08235
- Every structure of UniProt P36049
- Every structure of UniProt Q07915
- Every structure of UniProt P40007
- Every structure of UniProt Q12522
- Every structure of UniProt P14126
- Every structure of UniProt P10664
- Every structure of UniProt P38061
- Every structure of UniProt Q02326
- Every structure of UniProt P05744
- Every structure of UniProt P17076
- Every structure of UniProt P0CX84
- Every structure of UniProt O14455
- Every structure of UniProt P49166
- 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 P0CX23
- Every structure of UniProt P0CX41
- Every structure of UniProt P05743
- Every structure of UniProt Q03532
- Every structure of UniProt P38779
- Every structure of UniProt P53261
- Every structure of UniProt P53927
- Every structure of UniProt P40693
- Every structure of UniProt Q04660
- Elsewhere: RCSB PDB 6EM4 · PDBe 6EM4 · UniProt P38805 · UniProt P05737 · UniProt P10962 · UniProt P35178 · UniProt P53136 · UniProt Q08235 · UniProt P36049 · UniProt Q07915 · UniProt P40007 · UniProt Q12522 · UniProt P14126 · UniProt P10664 · UniProt P38061 · UniProt Q02326 · UniProt P05744 · UniProt P17076 · UniProt P0CX84 · UniProt O14455 · UniProt P49166 · UniProt Q12690 · UniProt P36105 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P0CX23 · UniProt P0CX41 · UniProt P05743 · UniProt Q03532 · UniProt P38779 · UniProt P53261 · UniProt P53927 · UniProt P40693 · UniProt Q04660
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