8K2D
Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A
This is a non-PDB format compatible entry.
Functional Information from PROSITE/UniProt
| site_id | PS00049 |
| Number of Residues | 27 |
| Details | RIBOSOMAL_L14 Ribosomal protein L14 signature. AIVVrqakswrrr.DGvflyFedNagVI |
| Chain | Residue | Details |
| LV | ALA76-ILE102 |
| site_id | PS00050 |
| Number of Residues | 16 |
| Details | RIBOSOMAL_L23 Ribosomal protein L23 signature. KKAYVRLTadydaldI |
| Chain | Residue | Details |
| LX | LYS120-ILE135 |
| site_id | PS00051 |
| Number of Residues | 17 |
| Details | RIBOSOMAL_L39E Ribosomal protein L39e signature. RTnntIryNakrRNWRR |
| Chain | Residue | Details |
| Ll | ARG30-ARG46 |
| site_id | PS00052 |
| Number of Residues | 27 |
| Details | RIBOSOMAL_S7 Ribosomal protein S7 signature. ErLtnsLMmngrnnGKKlkavrIIkhT |
| Chain | Residue | Details |
| SF | GLU91-THR117 |
| site_id | PS00053 |
| Number of Residues | 18 |
| Details | RIBOSOMAL_S8 Ribosomal protein S8 signature. GyvILTTSaGIMdheeAR |
| Chain | Residue | Details |
| SW | GLY100-ARG117 |
| site_id | PS00054 |
| Number of Residues | 23 |
| Details | RIBOSOMAL_S11 Ribosomal protein S11 signature. LrALarS.GLrIgrieDvTPvPSD |
| Chain | Residue | Details |
| SO | LEU102-ASP124 |
| site_id | PS00055 |
| Number of Residues | 8 |
| Details | RIBOSOMAL_S12 Ribosomal protein S12 signature. KqPNSAiR |
| Chain | Residue | Details |
| SX | LYS62-ARG69 |
| site_id | PS00056 |
| Number of Residues | 13 |
| Details | RIBOSOMAL_S17 Ribosomal protein S17 signature. GDiVtVgQcRPIS |
| Chain | Residue | Details |
| SL | GLY120-SER132 |
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KskIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| Lm | LYS27-ASP52 | |
| Sf | LYS27-ASP52 |
| site_id | PS00301 |
| Number of Residues | 16 |
| Details | G_TR_1 Translational (tr)-type guanine nucleotide-binding (G) domain signature. DTrkdEQeRGITIksT |
| Chain | Residue | Details |
| CD | ASP58-THR73 |
| site_id | PS00302 |
| Number of Residues | 8 |
| Details | IF5A_HYPUSINE Eukaryotic initiation factor 5A hypusine signature. TGKHGhAK |
| Chain | Residue | Details |
| CE | THR49-LYS56 |
| site_id | PS00323 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_S19 Ribosomal protein S19 signature. NGKafnqveIrpemLGhyLGEFsiT |
| Chain | Residue | Details |
| SP | ASN98-THR122 |
| site_id | PS00358 |
| Number of Residues | 17 |
| Details | RIBOSOMAL_L5 Ribosomal protein L5 signature. LeqLSGQtpVqSkARyT |
| Chain | Residue | Details |
| LJ | LEU37-THR53 |
| site_id | PS00359 |
| Number of Residues | 15 |
| Details | RIBOSOMAL_L11 Ribosomal protein L11 signature. KeIlGTaqSVGcRV.D |
| Chain | Residue | Details |
| LK | LYS130-ASP144 |
| site_id | PS00360 |
| Number of Residues | 19 |
| Details | RIBOSOMAL_S9 Ribosomal protein S9 signature. GGGhvSQvyAirqAiAKGL |
| Chain | Residue | Details |
| SQ | GLY71-LEU89 |
| site_id | PS00361 |
| Number of Residues | 16 |
| Details | RIBOSOMAL_S10 Ribosomal protein S10 signature. AeqhNLvkkGPVrLPT |
| Chain | Residue | Details |
| SU | ALA45-THR60 |
| site_id | PS00362 |
| Number of Residues | 31 |
| Details | RIBOSOMAL_S15 Ribosomal protein S15 signature. VrkHLernRkDkdAkfrLilIesrihrLarY |
| Chain | Residue | Details |
| SN | VAL98-TYR128 |
| site_id | PS00464 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_L22 Ribosomal protein L22 signature. RrrTyRAhGRinkyesspSHIELvV |
| Chain | Residue | Details |
| LP | ARG126-VAL150 |
| site_id | PS00467 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_L2 Ribosomal protein L2 signature. PktRGVAmNPvD |
| Chain | Residue | Details |
| LA | PRO197-ASP208 |
| site_id | PS00474 |
| Number of Residues | 24 |
| Details | RIBOSOMAL_L3 Ribosomal protein L3 signature. FeqnemiDaiAvTkGHGfeGvthR |
| Chain | Residue | Details |
| LB | PHE209-ARG232 |
| site_id | PS00475 |
| Number of Residues | 32 |
| Details | RIBOSOMAL_L15 Ribosomal protein L15 signature. KILGkGrIpnvp.ViVkarfVSklAeekIraaG |
| Chain | Residue | Details |
| La | LYS111-GLY142 |
| site_id | PS00526 |
| Number of Residues | 20 |
| Details | RIBOSOMAL_L19E Ribosomal protein L19e signature. QKRLaAsvvgVGkrkVWLDP |
| Chain | Residue | Details |
| LR | GLN7-PRO26 |
| site_id | PS00527 |
| Number of Residues | 23 |
| Details | RIBOSOMAL_S14 Ribosomal protein S14 signature. RvCsshtglirkyg.LNICRqCFR |
| Chain | Residue | Details |
| Sd | ARG22-ARG44 |
| site_id | PS00528 |
| Number of Residues | 15 |
| Details | RIBOSOMAL_S4E Ribosomal protein S4e signature. HlKRLAaPhhWlLdK |
| Chain | Residue | Details |
| SE | HIS8-LYS22 |
| site_id | PS00529 |
| Number of Residues | 23 |
| Details | RIBOSOMAL_S24E Ribosomal protein S24e signature. FGggKSvGFGlVYNSvaeakkfE |
| Chain | Residue | Details |
| SY | PHE64-GLU86 |
| site_id | PS00548 |
| Number of Residues | 37 |
| Details | RIBOSOMAL_S3 Ribosomal protein S3 signature. AKamkfadGfLihSgqpVndfIDtatrhvlMrqGvlG |
| Chain | Residue | Details |
| SD | ALA147-GLY183 |
| site_id | PS00578 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_S6E Ribosomal protein S6e signature. ISGGnDkqGfPM |
| Chain | Residue | Details |
| SG | ILE52-MET63 |
| site_id | PS00579 |
| Number of Residues | 15 |
| Details | RIBOSOMAL_L29 Ribosomal protein L29 signature. SLPKIKtVRKSIACV |
| Chain | Residue | Details |
| Lh | SER40-VAL54 |
| site_id | PS00580 |
| Number of Residues | 21 |
| Details | RIBOSOMAL_L32E Ribosomal protein L32e signature. FkRhhsdRyhRVaen..WRKqkG |
| Chain | Residue | Details |
| Le | PHE17-GLY37 |
| site_id | PS00585 |
| Number of Residues | 33 |
| Details | RIBOSOMAL_S5 Ribosomal protein S5 signature. GQrtrFkAvvVVGDsn.GhVGlGiktak.EVag.AI |
| Chain | Residue | Details |
| SC | GLY93-ILE125 |
| site_id | PS00628 |
| Number of Residues | 20 |
| Details | RIBOSOMAL_S19E Ribosomal protein S19e signature. PykhidaSgsInRkVLQaLE |
| Chain | Residue | Details |
| ST | PRO90-GLU109 |
| site_id | PS00632 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_S4 Ribosomal protein S4 signature. LErRLqtqVYKlglAkSvhhARvLI |
| Chain | Residue | Details |
| SJ | LEU105-ILE129 |
| site_id | PS00634 |
| Number of Residues | 33 |
| Details | RIBOSOMAL_L30 Ribosomal protein L30 signature. VLqlLrLtRinSgTfvkvtkatleLLklIepYV |
| Chain | Residue | Details |
| LF | VAL102-VAL134 |
| site_id | PS00646 |
| Number of Residues | 14 |
| Details | RIBOSOMAL_S13_1 Ribosomal protein S13 signature. RGiRHfwGlrVRGQ |
| Chain | Residue | Details |
| SS | ARG123-GLN136 |
| site_id | PS00678 |
| Number of Residues | 15 |
| Details | WD_REPEATS_1 Trp-Asp (WD) repeats signature. ALSAswDkTLRLWDV |
| Chain | Residue | Details |
| Sg | ALA80-VAL94 | |
| Sg | ILE169-LEU183 | |
| Sg | ILE211-LEU225 |
| site_id | PS00700 |
| Number of Residues | 22 |
| Details | RIBOSOMAL_L6_2 Ribosomal protein L6 signature 2. QicrVrnKdiRkFlDGIYVshK |
| Chain | Residue | Details |
| LH | GLN163-LYS184 |
| site_id | PS00709 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_L30E_1 Ribosomal protein L30e signature 1. SgkytlGyKstVKslRqGksKlIII |
| Chain | Residue | Details |
| Lc | SER20-ILE44 |
| site_id | PS00712 |
| Number of Residues | 16 |
| Details | RIBOSOMAL_S17E Ribosomal protein S17e signature. IqSKrLRNkIAGYtTH |
| Chain | Residue | Details |
| SR | ILE41-HIS56 |
| site_id | PS00733 |
| Number of Residues | 8 |
| Details | RIBOSOMAL_S26E Ribosomal protein S26e signature. YCVSCAIH |
| Chain | Residue | Details |
| Sa | TYR73-HIS80 |
| site_id | PS00783 |
| Number of Residues | 24 |
| Details | RIBOSOMAL_L13 Ribosomal protein L13 signature. LRGMVShktarGKaalerLkVFeG |
| Chain | Residue | Details |
| LO | LEU84-GLY107 |
| site_id | PS00939 |
| Number of Residues | 27 |
| Details | RIBOSOMAL_L1E Ribosomal protein L1e signature. NhneKryATaSAIaATAvaslvlaRGH |
| Chain | Residue | Details |
| LC | ASN114-HIS140 |
| site_id | PS00948 |
| Number of Residues | 14 |
| Details | RIBOSOMAL_S7E Ribosomal protein S7e signature. KLtRELEKKFQdRH |
| Chain | Residue | Details |
| SH | LYS76-HIS89 |
| site_id | PS00961 |
| Number of Residues | 9 |
| Details | RIBOSOMAL_S28E Ribosomal protein S28e signature. ESEREARrL |
| Chain | Residue | Details |
| Sc | GLU58-LEU66 |
| site_id | PS00962 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_S2_1 Ribosomal protein S2 signature 1. AqLLLAANTHLG |
| Chain | Residue | Details |
| SA | ALA14-GLY25 |
| site_id | PS00963 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_S2_2 Ribosomal protein S2 signature 2. PrlVIVtDprsDaqaIkEasyvNIP |
| Chain | Residue | Details |
| SA | PRO118-PRO142 |
| site_id | PS00993 |
| Number of Residues | 21 |
| Details | RIBOSOMAL_L30E_2 Ribosomal protein L30e signature 2. ELGTavGKlfrvgvVsIlEaG |
| Chain | Residue | Details |
| Lc | GLU76-GLY96 |
| site_id | PS00996 |
| Number of Residues | 9 |
| Details | RIBOSOMAL_S21E Ribosomal protein S21e signature. LYVPRKCSA |
| Chain | Residue | Details |
| SV | LEU11-ALA19 |
| site_id | PS01073 |
| Number of Residues | 18 |
| Details | RIBOSOMAL_L24E Ribosomal protein L24e signature. FsGakIyPGrGtlFvRgD |
| Chain | Residue | Details |
| LW | PHE8-ASP25 |
| site_id | PS01077 |
| Number of Residues | 20 |
| Details | RIBOSOMAL_L37E Ribosomal protein L37e signature. GTpSfGkRhnks.HtlCnRCG |
| Chain | Residue | Details |
| Lj | GLY4-GLY23 |
| site_id | PS01082 |
| Number of Residues | 18 |
| Details | RIBOSOMAL_L7AE Ribosomal protein L7Ae signature. CkkmgVPYaiVkGKarLG |
| Chain | Residue | Details |
| LG | CYS170-GLY187 |
| site_id | PS01104 |
| Number of Residues | 15 |
| Details | RIBOSOMAL_L13E Ribosomal protein L13e signature. RaGRGFTLaEVkaaG |
| Chain | Residue | Details |
| LL | ARG70-GLY84 |
| site_id | PS01105 |
| Number of Residues | 22 |
| Details | RIBOSOMAL_L35AE Ribosomal protein L35Ae signature. GKVtRtHGnsGvVrAtFrnnLP |
| Chain | Residue | Details |
| Lf | GLY69-PRO90 |
| site_id | PS01106 |
| Number of Residues | 18 |
| Details | RIBOSOMAL_L18E Ribosomal protein L18e signature. KaLflSKinRPpVSVsRI |
| Chain | Residue | Details |
| LQ | LYS50-ILE67 |
| site_id | PS01107 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_L27E Ribosomal protein L27e signature. GKNqWFFskLRF |
| Chain | Residue | Details |
| LZ | GLY125-PHE136 |
| site_id | PS01108 |
| Number of Residues | 18 |
| Details | RIBOSOMAL_L24 Ribosomal protein L24 signature. DDeVlVVrGskKGqe.GkI |
| Chain | Residue | Details |
| LY | ASP53-ILE70 |
| site_id | PS01144 |
| Number of Residues | 15 |
| Details | RIBOSOMAL_L31E Ribosomal protein L31e signature. VRLApeLNqAiWkRG |
| Chain | Residue | Details |
| Ld | VAL49-GLY63 |
| site_id | PS01145 |
| Number of Residues | 14 |
| Details | RIBOSOMAL_L34E Ribosomal protein L34e signature. TrSnKikvvKTPGG |
| Chain | Residue | Details |
| Lg | THR15-GLY28 |
| site_id | PS01168 |
| Number of Residues | 33 |
| Details | RIBOSOMAL_S27E Ribosomal protein S27e signature. KCpgClnittvFShAqtavtCesCStiLctPtG |
| Chain | Residue | Details |
| Sb | LYS36-GLY68 |
| site_id | PS01170 |
| Number of Residues | 19 |
| Details | RIBOSOMAL_L6E Ribosomal protein L6e signature. NgvPLRRvnarYVIATSt.K |
| Chain | Residue | Details |
| LE | ASN72-LYS90 |
| site_id | PS01171 |
| Number of Residues | 26 |
| Details | RIBOSOMAL_L21E Ribosomal protein L21e signature. GDiVdikangsiqk.GmpHkfYqGkTG |
| Chain | Residue | Details |
| LT | GLY37-GLY62 |
| site_id | PS01172 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_L44E Ribosomal protein L44e signature. KtTKKvvLRleC |
| Chain | Residue | Details |
| Lo | LYS63-CYS74 |
| site_id | PS01189 |
| Number of Residues | 19 |
| Details | RIBOSOMAL_S12E Ribosomal protein S12e signature. ALKvvLrtAlvhDGLarGL |
| Chain | Residue | Details |
| SM | ALA27-LEU45 |
| site_id | PS01190 |
| Number of Residues | 11 |
| Details | RIBOSOMAL_L36E Ribosomal protein L36e signature. PYERRlIDLIR |
| Chain | Residue | Details |
| Li | PRO52-ARG62 |
| site_id | PS01191 |
| Number of Residues | 13 |
| Details | RIBOSOMAL_S3AE Ribosomal protein S3Ae signature. LkGRVvEvCLaDL |
| Chain | Residue | Details |
| SB | LEU61-LEU73 |
| site_id | PS01193 |
| Number of Residues | 20 |
| Details | RIBOSOMAL_S8E Ribosomal protein S8e signature. RsaTGAkraqf.RkKrKfELG |
| Chain | Residue | Details |
| SI | ARG11-GLY30 |
| site_id | PS01194 |
| Number of Residues | 24 |
| Details | RIBOSOMAL_L15E Ribosomal protein L15e signature. DKARrLGYkAkqGFVIYRvRVrRG |
| Chain | Residue | Details |
| LN | ASP46-GLY69 |
| site_id | PS01199 |
| Number of Residues | 20 |
| Details | RIBOSOMAL_L1 Ribosomal protein L1 signature. IkqVprlLGpqLSKAGkFPT |
| Chain | Residue | Details |
| L1 | ILE117-THR136 |
| site_id | PS01257 |
| Number of Residues | 22 |
| Details | RIBOSOMAL_L10E Ribosomal protein L10e signature. ADRlqqGMRgAWGKPhGlaARV |
| Chain | Residue | Details |
| LI | ALA108-VAL129 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | MOD_RES: N-acetylserine => ECO:0000269|Ref.7 |
| Chain | Residue | Details |
| CS | SER2 | |
| Lh | SER50 | |
| Lc | LYS53 | |
| Lc | LYS83 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 5 |
| Details | MOD_RES: Phosphoserine; by MTOR => ECO:0000269|PubMed:36691768 |
| Chain | Residue | Details |
| CS | SER32 | |
| SL | LYS141 | |
| SL | LYS148 | |
| CS | SER41 | |
| CS | SER45 | |
| CS | SER55 | |
| CS | SER73 | |
| LR | LYS186 | |
| SL | LYS96 | |
| SL | LYS105 | |
| SL | LYS133 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| CS | SER118 | |
| Sf | LYS113 | |
| SU | LYS21 | |
| P0 | LYS97 | |
| P0 | LYS144 | |
| LA | LYS145 | |
| Sf | LYS33 | |
| Sf | LYS48 | |
| Sf | LYS63 | |
| Sf | LYS107 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by MTOR => ECO:0000269|PubMed:36691768 |
| Chain | Residue | Details |
| CS | THR181 | |
| CS | THR218 | |
| Sg | LYS53 | |
| Sg | LYS107 | |
| Sg | LYS137 | |
| Sg | LYS161 | |
| SE | LYS179 | |
| SE | LYS211 | |
| SE | LYS233 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17287358 |
| Chain | Residue | Details |
| CS | SER229 | |
| LB | LYS136 | |
| SQ | LYS59 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 5 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047 |
| Chain | Residue | Details |
| CS | LYS46 | |
| CS | LYS121 | |
| CS | LYS171 | |
| CS | LYS184 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| CD | THR713 | |
| CD | THR763 | |
| LK | LYS146 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047 |
| Chain | Residue | Details |
| CD | LYS841 | |
| SD | LYS132 | |
| SD | LYS141 | |
| SD | LYS151 | |
| SD | LYS200 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:28757607, ECO:0000269|PubMed:30718516, ECO:0000269|PubMed:30893611, ECO:0000269|PubMed:31819057, ECO:0007744|PubMed:22106047 |
| Chain | Residue | Details |
| SD | LYS212 |
