Research workbench
Structure of a partial yeast 48S preinitiation complex in open conformation.
Analyse Structure of a partial yeast 48S preinitiation complex in open conformation. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GSM
- Type
- protein + RNA
- Length
- 9,927 residues
- Chains
- 47
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.15
- Source
- Kluyveromyces lactis NRRL Y-1140; Saccharomyces cerevisiae S288C; SYNTHETIC…
- Molecule
- Met-tRNAi; 18S ribosomal RNA; 40S ribosomal protein S0; mRNA (5'-R(P*AP*AP*U)-3'); 40S…
- UniProt
- Q6CN12, Q6CWD0, Q6CKL3, Q6CRK7, Q6CWJ2, Q6CRA3, Q6CM04, Q6CTD6, Q6CMG3, Q6CM18, Q6CVZ5, Q6CX80, Q6CLU4, Q6CJK0, P27069, Q6CKV4, Q875N2, Q6CWU3, Q6CWT9, Q6CXM0, Q6CIM1, Q6CXT6, Q6CW21, F2Z602, Q6CU44, Q6CW78, Q6CS01, Q6CNL2, P33285, Q6CPG3, Q6CUH5, P69061, Q6CNI7, P0CX86, P38912, P20459, P32481, P09064, P32911, P38249, P06103, P32497, P40217, Q04067
- Ligands
- 7NO, GCP, MG, ZN
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · resolution 5.15 · 47 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Met-tRNAi | rna | 74 | — | — |
| 2 | 18S ribosomal RNA | rna | 1798 | — | — |
| A | 40S ribosomal protein S0 | protein | 208 | 32% helix, 11% strand | Q6CN12 |
| 3 | mRNA (5'-R(P*AP*AP*U)-3') | rna | 3 | — | — |
| B | 40S ribosomal protein S1 | protein | 222 | 26% helix, 32% strand | Q6CWD0 |
| C | KLLA0F09812p | protein | 217 | 29% helix, 25% strand | Q6CKL3 |
| D | KLLA0D08305p | protein | 223 | 31% helix, 23% strand | Q6CRK7 |
| E | 40S ribosomal protein S4 | protein | 260 | 13% helix, 32% strand | Q6CWJ2 |
| F | KLLA0D10659p | protein | 206 | 48% helix, 3% strand | Q6CRA3 |
| G | 40S ribosomal protein S6 | protein | 226 | 23% helix, 24% strand | Q6CM04 |
| H | 40S ribosomal protein S7 | protein | 184 | 34% helix, 20% strand | Q6CTD6 |
| I | 40S ribosomal protein S8 | protein | 188 | 29% helix, 23% strand | Q6CMG3 |
| J | KLLA0E23673p | protein | 182 | 49% helix, 3% strand | Q6CM18 |
| K | KLLA0B08173p | protein | 96 | 44% helix, 6% strand | Q6CVZ5 |
| L | KLLA0A10483p | protein | 155 | 3% helix, 25% strand | Q6CX80 |
| M | 40S ribosomal protein S12 | protein | 117 | 37% helix, 6% strand | Q6CLU4 |
| N | KLLA0F18040p | protein | 150 | 55% helix, 0% strand | Q6CJK0 |
| O | 40S ribosomal protein S14 | protein | 127 | 28% helix, 25% strand | P27069 |
| P | KLLA0F07843p | protein | 119 | 20% helix, 13% strand | Q6CKV4 |
| Q | 40S ribosomal protein S16 | protein | 141 | 31% helix, 11% strand | Q875N2 |
| R | KLLA0B01474p | protein | 111 | 50% helix, 3% strand | Q6CWU3 |
| S | KLLA0B01562p | protein | 145 | 30% helix, 4% strand | Q6CWT9 |
| T | KLLA0A07194p | protein | 143 | 47% helix, 10% strand | Q6CXM0 |
| U | KLLA0F25542p | protein | 106 | 25% helix, 37% strand | Q6CIM1 |
| V | 40S ribosomal protein S21 | protein | 87 | 24% helix, 22% strand | Q6CXT6 |
| W | 40S ribosomal protein S22 | protein | 129 | 33% helix, 26% strand | Q6CW21 |
| X | KLLA0B11231p | protein | 144 | 22% helix, 26% strand | F2Z602 |
| Y | 40S ribosomal protein S24 | protein | 134 | 37% helix, 22% strand | Q6CU44 |
| Z | KLLA0B06182p | protein | 70 | 39% helix, 9% strand | Q6CW78 |
| a | 40S ribosomal protein S26 | protein | 98 | 14% helix, 6% strand | Q6CS01 |
| b | 40S ribosomal protein S27 | protein | 81 | 7% helix, 16% strand | Q6CNL2 |
| c | 40S ribosomal protein S28 | protein | 62 | 0% helix, 47% strand | P33285 |
| d | 40S ribosomal protein S29 | protein | 53 | 19% helix, 2% strand | Q6CPG3 |
| e | 40S ribosomal protein S30 | protein | 58 | 22% helix, 0% strand | Q6CUH5 |
| f | Ubiquitin-40S ribosomal protein S27a | protein | 69 | 0% helix, 3% strand | P69061 |
| g | KLLA0E12277p | protein | 309 | 1% helix, 59% strand | Q6CNI7 |
| h | 60S ribosomal protein L41-A | protein | 25 | 76% helix, 0% strand | P0CX86 |
| i | Eukaryotic translation initiation factor 1A | protein | 95 | 15% helix, 29% strand | P38912 |
| j | Eukaryotic translation initiation factor 2 subunit alpha | protein | 249 | 16% helix, 13% strand | P20459 |
| k | Eukaryotic translation initiation factor 2 subunit gamma | protein | 414 | 10% helix, 17% strand | P32481 |
| l | Eukaryotic translation initiation factor 2 subunit beta | protein | 130 | 20% helix, 12% strand | P09064 |
| m | Eukaryotic translation initiation factor eIF-1 | protein | 96 | 10% helix, 21% strand | P32911 |
| o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A,eIF3a | protein | 528 | 39% helix, 0% strand | P38249 |
| p | Eukaryotic translation initiation factor 3 subunit B | protein | 651 | 10% helix, 22% strand | P06103 |
| q | Eukaryotic translation initiation factor 3 subunit C | protein | 665 | 26% helix, 0% strand | P32497 |
| s | Eukaryotic translation initiation factor 3 subunit I | protein | 330 | 6% helix, 52% strand | P40217 |
| r | Eukaryotic translation initiation factor 3 subunit G | protein | 49 | 35% helix, 6% strand | Q04067 |
Ligands and binding sites
- 7NO · [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate · ligand · chains 1, k
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains k, l
- MG · Magnesium ion · metal · 82 copies · chains 2, X, O, G, p, D, T, U, C, Q, k
- ZN · Zinc ion · metal · 4 copies · chains O, a, b, q, f, k, l
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 | 942 | 0.90 | 0.93 | 101 | MG |
| 2 | 1137 | 0.88 | 0.90 | 122 | MG |
| 3 | 877 | 0.87 | 0.90 | 93 | MG |
| 4 | 728 | 0.87 | 0.91 | 72 | MG |
| 5 | 920 | 0.87 | 0.89 | 70 | MG |
Interfaces
134 interfaces between chains.
- 2–G · 5264 Ų buried · 88 hydrogen bonds · protein-nucleic
- 2–E · 4582 Ų buried · 69 hydrogen bonds · protein-nucleic
- 2–I · 4125 Ų buried · 93 hydrogen bonds · protein-nucleic
- 2–X · 3901 Ų buried · 82 hydrogen bonds · protein-nucleic
- 2–J · 3787 Ų buried · 73 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 11 modified, 1 covalent, 1 isopeptide (nucleotide modification, covalent ligand, isopeptide).
Compared structures
- P40217 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain s against A, TM-score 0.99
- Q04067 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain r against A, TM-score 0.97
- Q6CW21 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22 (Q6CW21) · a predicted model of the same protein · chain W against A, TM-score 0.97
- Q6CN12 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S0 (Q6CN12) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P27069 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14 (P27069) · a predicted model of the same protein · chain O against A, TM-score 0.95
- Q6CM04 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S6 (Q6CM04) · a predicted model of the same protein · chain G against A, TM-score 0.94
- Q6CXT6 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S21 (Q6CXT6) · a predicted model of the same protein · chain V against A, TM-score 0.93
- P32481 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain k against A, TM-score 0.92
- Q875N2 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S16 (Q875N2) · a predicted model of the same protein · chain Q against A, TM-score 0.92
- Q6CWD0 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S1 (Q6CWD0) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P20459 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain j against A, TM-score 0.89
- P38912 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 1A (P38912) · a predicted model of the same protein · chain i against A, TM-score 0.88
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 Q6CN12
- Every structure of UniProt Q6CWD0
- Every structure of UniProt Q6CKL3
- Every structure of UniProt Q6CRK7
- Every structure of UniProt Q6CWJ2
- Every structure of UniProt Q6CRA3
- Every structure of UniProt Q6CM04
- Every structure of UniProt Q6CTD6
- Every structure of UniProt Q6CMG3
- Every structure of UniProt Q6CM18
- Every structure of UniProt Q6CVZ5
- Every structure of UniProt Q6CX80
- Every structure of UniProt Q6CLU4
- Every structure of UniProt Q6CJK0
- Every structure of UniProt P27069
- Every structure of UniProt Q6CKV4
- Every structure of UniProt Q875N2
- Every structure of UniProt Q6CWU3
- Every structure of UniProt Q6CWT9
- Every structure of UniProt Q6CXM0
- Every structure of UniProt Q6CIM1
- Every structure of UniProt Q6CXT6
- Every structure of UniProt Q6CW21
- Every structure of UniProt F2Z602
- Every structure of UniProt Q6CU44
- Every structure of UniProt Q6CW78
- Every structure of UniProt Q6CS01
- Every structure of UniProt Q6CNL2
- Every structure of UniProt P33285
- Every structure of UniProt Q6CPG3
- Every structure of UniProt Q6CUH5
- Every structure of UniProt P69061
- Every structure of UniProt Q6CNI7
- Every structure of UniProt P0CX86
- Every structure of UniProt P38912
- Every structure of UniProt P20459
- Every structure of UniProt P32481
- Every structure of UniProt P09064
- Every structure of UniProt P32911
- Every structure of UniProt P38249
- Every structure of UniProt P06103
- Every structure of UniProt P32497
- Every structure of UniProt P40217
- Every structure of UniProt Q04067
- Elsewhere: RCSB PDB 6GSM · PDBe 6GSM · UniProt Q6CN12 · UniProt Q6CWD0 · UniProt Q6CKL3 · UniProt Q6CRK7 · UniProt Q6CWJ2 · UniProt Q6CRA3 · UniProt Q6CM04 · UniProt Q6CTD6 · UniProt Q6CMG3 · UniProt Q6CM18 · UniProt Q6CVZ5 · UniProt Q6CX80 · UniProt Q6CLU4 · UniProt Q6CJK0 · UniProt P27069 · UniProt Q6CKV4 · UniProt Q875N2 · UniProt Q6CWU3 · UniProt Q6CWT9 · UniProt Q6CXM0 · UniProt Q6CIM1 · UniProt Q6CXT6 · UniProt Q6CW21 · UniProt F2Z602 · UniProt Q6CU44 · UniProt Q6CW78 · UniProt Q6CS01 · UniProt Q6CNL2 · UniProt P33285 · UniProt Q6CPG3 · UniProt Q6CUH5 · UniProt P69061 · UniProt Q6CNI7 · UniProt P0CX86 · UniProt P38912 · UniProt P20459 · UniProt P32481 · UniProt P09064 · UniProt P32911 · UniProt P38249 · UniProt P06103 · UniProt P32497 · UniProt P40217 · UniProt Q04067
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