8K2A
Cryo-EM structure of the human 55S mitoribosome with Tigecycline
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | L1 | 16S rRNA | polymer | 1559 | 500019.6 | 1 | Homo sapiens (human) | ||
| 2 | L2 | Val tRNA | polymer | 69 | 22022.1 | 1 | Homo sapiens (human) | ||
| 3 | LB | Large ribosomal subunit protein uL2m | polymer | 305 | 33355.9 | 1 | UniProt (Q5T653) In PDB | Homo sapiens (human) | 39S ribosomal protein L2,mitochondrial,L2mt,MRP-L2 |
| 4 | LC | Large ribosomal subunit protein uL3m | polymer | 348 | 38689.6 | 1 | UniProt (P09001) In PDB | Homo sapiens (human) | 39S ribosomal protein L3,mitochondrial,L3mt,MRP-L3 |
| 5 | LD | Large ribosomal subunit protein uL4m | polymer | 311 | 34970.2 | 1 | UniProt (Q9BYD3) In PDB | Homo sapiens (human) | 39S ribosomal protein L4,mitochondrial,L4mt,MRP-L4 |
| 6 | LI | Large ribosomal subunit protein bL9m | polymer | 267 | 30296.4 | 1 | UniProt (Q9BYD2) In PDB | Homo sapiens (human) | 39S ribosomal protein L9,mitochondrial,L9mt,MRP-L9 |
| 7 | LJ | Large ribosomal subunit protein uL10m | polymer | 261 | 29322.5 | 1 | UniProt (Q7Z7H8) In PDB | Homo sapiens (human) | 39S ribosomal protein L10,mitochondrial,L10mt,MRP-L10,39S ribosomal protein L8,L8mt,MRP-L8 |
| 8 | LK | Large ribosomal subunit protein uL11m | polymer | 192 | 20716.2 | 1 | UniProt (Q9Y3B7) In PDB | Homo sapiens (human) | 39S ribosomal protein L11,mitochondrial,L11mt,MRP-L11 |
| 9 | LM | Large ribosomal subunit protein uL13m | polymer | 178 | 20723.0 | 1 | UniProt (Q9BYD1) In PDB | Homo sapiens (human) | 39S ribosomal protein L13,mitochondrial,L13mt,MRP-L13 |
| 10 | LN | Large ribosomal subunit protein uL14m | polymer | 145 | 15973.7 | 1 | UniProt (Q6P1L8) In PDB | Homo sapiens (human) | 39S ribosomal protein L14,mitochondrial,L14mt,MRP-L14,39S ribosomal protein L32,L32mt,MRP-L32 |
| 11 | LO | Large ribosomal subunit protein uL15m | polymer | 296 | 33473.8 | 1 | UniProt (Q9P015) In PDB | Homo sapiens (human) | 39S ribosomal protein L15,mitochondrial,L15mt,MRP-L15 |
| 12 | LP | Large ribosomal subunit protein uL16m | polymer | 251 | 28496.3 | 1 | UniProt (Q9NX20) In PDB | Homo sapiens (human) | 39S ribosomal protein L16,mitochondrial,L16mt,MRP-L16 |
| 13 | LQ | Large ribosomal subunit protein bL17m | polymer | 175 | 20083.3 | 1 | UniProt (Q9NRX2) In PDB | Homo sapiens (human) | 39S ribosomal protein L17,mitochondrial,L17mt,MRP-L17,LYST-interacting protein 2 |
| 14 | LR | Mitochondrial ribosomal protein L18, isoform CRA_b | polymer | 179 | 20465.3 | 1 | UniProt (A8K9D2) In PDB | Homo sapiens (human) | cDNA FLJ76688,highly similar to Homo sapiens HSPC071 mRNA |
| 15 | LS | Large ribosomal subunit protein bL19m | polymer | 292 | 33585.0 | 1 | UniProt (P49406) In PDB | Homo sapiens (human) | 39S ribosomal protein L15,mitochondrial,L15mt,MRP-L15,39S ribosomal protein L19,L19mt,MRP-L19 |
| 16 | LT | Large ribosomal subunit protein bL20m | polymer | 149 | 17479.7 | 1 | UniProt (Q9BYC9) In PDB | Homo sapiens (human) | 39S ribosomal protein L20,mitochondrial,L20mt,MRP-L20 |
| 17 | LU | Large ribosomal subunit protein bL21m | polymer | 205 | 22847.7 | 1 | UniProt (Q7Z2W9) In PDB | Homo sapiens (human) | 39S ribosomal protein L21,mitochondrial,L21mt,MRP-L21 |
| 18 | LV | 39S ribosomal protein L22, mitochondrial | polymer | 212 | 24369.5 | 1 | UniProt (E7ESL0) In PDB | Homo sapiens (human) | |
| 19 | LW | Large ribosomal subunit protein uL23m | polymer | 153 | 17807.2 | 1 | UniProt (Q16540) In PDB | Homo sapiens (human) | 39S ribosomal protein L23,mitochondrial,L23mt,MRP-L23,L23 mitochondrial-related protein,Ribosomal protein L23-like |
| 20 | LX | Large ribosomal subunit protein uL24m | polymer | 216 | 24953.9 | 1 | UniProt (Q96A35) In PDB | Homo sapiens (human) | 39S ribosomal protein L24,mitochondrial,L24mt,MRP-L24 |
| 21 | La | Large ribosomal subunit protein bL27m | polymer | 148 | 16102.9 | 1 | UniProt (Q9P0M9) In PDB | Homo sapiens (human) | 39S ribosomal protein L27,mitochondrial,L27mt,MRP-L27 |
| 22 | Lb | Large ribosomal subunit protein bL28m | polymer | 256 | 30202.9 | 1 | UniProt (Q13084) In PDB | Homo sapiens (human) | 39S ribosomal protein L28,mitochondrial,L28mt,MRP-L28,Melanoma antigen p15,Melanoma-associated antigen recognized by T-lymphocytes |
| 23 | Lu | Large ribosomal subunit protein uL29m | polymer | 250 | 29508.5 | 1 | UniProt (Q9HD33) In PDB | Homo sapiens (human) | 39S ribosomal protein L47,mitochondrial,L47mt,MRP-L47,Nasopharyngeal carcinoma metastasis-related protein 1 |
| 24 | Ld | Large ribosomal subunit protein uL30m | polymer | 161 | 18582.8 | 1 | UniProt (Q8TCC3) In PDB | Homo sapiens (human) | 39S ribosomal protein L28,mitochondrial,L28mt,MRP-L28,39S ribosomal protein L30,L30mt,MRP-L30 |
| 25 | Lf | Large ribosomal subunit protein bL32m | polymer | 188 | 21437.8 | 1 | UniProt (Q9BYC8) In PDB | Homo sapiens (human) | 39S ribosomal protein L32,mitochondrial,L32mt,MRP-L32 |
| 26 | Lg | Large ribosomal subunit protein bL33m | polymer | 65 | 7635.2 | 1 | UniProt (O75394) In PDB | Homo sapiens (human) | 39S ribosomal protein L33,mitochondrial,L33mt,MRP-L33 |
| 27 | Lh | Large ribosomal subunit protein bL34m | polymer | 92 | 10183.9 | 1 | UniProt (Q9BQ48) In PDB | Homo sapiens (human) | 39S ribosomal protein L34,mitochondrial,L34mt,MRP-L34 |
| 28 | Li | Large ribosomal subunit protein bL35m | polymer | 188 | 21558.5 | 1 | UniProt (Q9NZE8) In PDB | Homo sapiens (human) | 39S ribosomal protein L35,mitochondrial,L35mt,MRP-L35 |
| 29 | Lj | Large ribosomal subunit protein bL36m | polymer | 103 | 11809.3 | 1 | UniProt (Q9P0J6) In PDB | Homo sapiens (human) | 39S ribosomal protein L36,mitochondrial,L36mt,MRP-L36,BRCA1-interacting protein 1 |
| 30 | Lk | Large ribosomal subunit protein mL37 | polymer | 423 | 48183.3 | 1 | UniProt (Q9BZE1) In PDB | Homo sapiens (human) | 39S ribosomal protein L2,mitochondrial,L2mt,MRP-L2,39S ribosomal protein L37,L37mt,MRP-L37 |
| 31 | Ll | Large ribosomal subunit protein mL38 | polymer | 380 | 44659.4 | 1 | UniProt (Q96DV4) In PDB | Homo sapiens (human) | 39S ribosomal protein L38,mitochondrial,L38mt,MRP-L38 |
| 32 | Lm | Large ribosomal subunit protein mL39 | polymer | 338 | 38764.8 | 1 | UniProt (Q9NYK5) In PDB | Homo sapiens (human) | 39S ribosomal protein L39,mitochondrial,L39mt,MRP-L39,39S ribosomal protein L5,L5mt,MRP-L5 |
| 33 | Ln | Large ribosomal subunit protein mL40 | polymer | 206 | 24534.4 | 1 | UniProt (Q9NQ50) In PDB | Homo sapiens (human) | 39S ribosomal protein L40,mitochondrial,L40mt,MRP-L40,Nuclear localization signal-containing protein deleted in velocardiofacial syndrome,Up-regulated in metastasis |
| 34 | Lo | Large ribosomal subunit protein mL41 | polymer | 137 | 15404.7 | 1 | UniProt (Q8IXM3) In PDB | Homo sapiens (human) | 39S ribosomal protein L41,mitochondrial,L41mt,MRP-L41,Bcl-2-interacting mitochondrial ribosomal protein L41,Cell proliferation-inducing gene 3 protein,MRP-L27 homolog |
| 35 | Lp | Large ribosomal subunit protein mL42 | polymer | 142 | 16691.2 | 1 | UniProt (Q9Y6G3) In PDB | Homo sapiens (human) | 39S ribosomal protein L31,mitochondrial,L31mt,MRP-L31,39S ribosomal protein L42,L42mt,MRP-L42 |
| 36 | Lq | Large ribosomal subunit protein mL43 | polymer | 215 | 23457.8 | 1 | UniProt (Q8N983) In PDB | Homo sapiens (human) | 39S ribosomal protein L43,mitochondrial,L43mt,MRP-L43,Mitochondrial ribosomal protein bMRP36a |
| 37 | Lr | Large ribosomal subunit protein mL44 | polymer | 332 | 37583.3 | 1 | UniProt (Q9H9J2) In PDB | Homo sapiens (human) | 39S ribosomal protein L44,mitochondrial,L44mt,MRP-L44 |
| 38 | Ls | Large ribosomal subunit protein mL45 | polymer | 306 | 35402.9 | 1 | UniProt (Q9BRJ2) In PDB | Homo sapiens (human) | 39S ribosomal protein L45,mitochondrial,L45mt,MRP-L45 |
| 39 | Lt | Large ribosomal subunit protein mL46 | polymer | 279 | 31748.1 | 1 | UniProt (Q9H2W6) In PDB | Homo sapiens (human) | 39S ribosomal protein L46,mitochondrial,L46mt,MRP-L46,P2ECSL |
| 40 | Lv | Large ribosomal subunit protein mL48 | polymer | 212 | 23970.8 | 1 | UniProt (Q96GC5) In PDB | Homo sapiens (human) | 39S ribosomal protein L48,mitochondrial,L48mt,MRP-L48 |
| 41 | Lw | Large ribosomal subunit protein mL49 | polymer | 166 | 19225.0 | 1 | UniProt (Q13405) In PDB | Homo sapiens (human) | 39S ribosomal protein L49,mitochondrial,L49mt,MRP-L49,Neighbor of FAU,NOF,Protein NOF1 |
| 42 | Lx | Large ribosomal subunit protein mL50 | polymer | 158 | 18349.9 | 1 | UniProt (Q8N5N7) In PDB | Homo sapiens (human) | 39S ribosomal protein L50,mitochondrial,L50mt,MRP-L50 |
| 43 | Ly | Large ribosomal subunit protein mL51 | polymer | 128 | 15125.9 | 1 | UniProt (Q4U2R6) In PDB | Homo sapiens (human) | 39S ribosomal protein L51,mitochondrial,L51mt,MRP-L51,bMRP-64,bMRP64 |
| 44 | Lz | 39S ribosomal protein L52, mitochondrial | polymer | 123 | 13696.7 | 1 | UniProt (A8K7J6) In PDB | Homo sapiens (human) | |
| 45 | L3 | Large ribosomal subunit protein mL53 | polymer | 112 | 12125.9 | 1 | UniProt (Q96EL3) In PDB | Homo sapiens (human) | 39S ribosomal protein L53,mitochondrial,L53mt,MRP-L53 |
| 46 | L4 | Large ribosomal subunit protein mL54 | polymer | 138 | 15844.2 | 1 | UniProt (Q6P161) In PDB | Homo sapiens (human) | 39S ribosomal protein L54,mitochondrial,L54mt,MRP-L54 |
| 47 | L5 | Large ribosomal subunit protein mL55 | polymer | 128 | 15160.4 | 1 | UniProt (Q7Z7F7) In PDB | Homo sapiens (human) | 39S ribosomal protein L55,mitochondrial,L55mt,MRP-L55,Mitochondrial large ribosomal subunit protein bL31m |
| 48 | L6 | Large ribosomal subunit protein mL63 | polymer | 102 | 12292.3 | 1 | UniProt (Q9BQC6) In PDB | Homo sapiens (human) | Mitochondrial ribosomal protein 63,Mitochondrial ribosomal protein L57,Ribosomal protein 63,mitochondrial,hMRP63 |
| 49 | L7 | Large ribosomal subunit protein mL62 | polymer | 206 | 23674.2 | 1 | UniProt (Q14197) In PDB | Homo sapiens (human) | 39S ribosomal protein L58,mitochondrial,MRP-L58,Digestion substraction 1,DS-1,Immature colon carcinoma transcript 1 protein,Peptidyl-tRNA hydrolase ICT1 |
| 50 | L8 | Large ribosomal subunit protein mL64 | polymer | 222 | 25426.9 | 1 | UniProt (Q8TAE8) In PDB | Homo sapiens (human) | 39S ribosomal protein L59,mitochondrial,MRP-L59,CKII beta-associating protein,CR6-interacting factor 1,CRIF1,Growth arrest and DNA damage-inducible proteins-interacting protein 1,Papillomavirus L2-interacting nuclear protein 1,PLINP,PLINP-1,p53-responsive gene 6 protein |
| 51 | SR | Large ribosomal subunit protein mL66 | polymer | 196 | 22224.1 | 1 | UniProt (Q9NVS2) In PDB | Homo sapiens (human) | 39S ribosomal protein S18-3,mitochondrial,MRP-S18-3,39S ribosomal protein S18a,MRP-S18-a,Mrps18a,S18mt-a,Large ribosomal subunit protein bS18a |
| 52 | Sf | Large ribosomal subunit protein mL65 | polymer | 439 | 50429.6 | 1 | UniProt (Q9NP92) In PDB | Homo sapiens (human) | 39S ribosomal protein S30,mitochondrial,MRP-S30,S30mt,Large ribosomal subunit protein mS30,Programmed cell death protein 9 |
| 53 | SB | Small ribosomal subunit protein uS2m | polymer | 296 | 33298.2 | 1 | UniProt (Q9Y399) In PDB | Homo sapiens (human) | 28S ribosomal protein S2,mitochondrial,MRP-S2,S2mt |
| 54 | SZ | Small ribosomal subunit protein uS3m | polymer | 167 | 19046.2 | 1 | UniProt (Q96EL2) In PDB | Homo sapiens (human) | 28S ribosomal protein S24,mitochondrial,MRP-S24,S24mt,bMRP-47,bMRP47 |
| 55 | SE | Small ribosomal subunit protein uS5m | polymer | 430 | 48094.6 | 1 | UniProt (P82675) In PDB | Homo sapiens (human) | 28S ribosomal protein S5,mitochondrial,MRP-S5,S5mt |
| 56 | SF | Small ribosomal subunit protein bS6m | polymer | 125 | 14250.6 | 1 | UniProt (P82932) In PDB | Homo sapiens (human) | 28S ribosomal protein S6,mitochondrial,MRP-S6,S6mt |
| 57 | SG | Small ribosomal subunit protein uS7m | polymer | 242 | 28186.2 | 1 | UniProt (Q9Y2R9) In PDB | Homo sapiens (human) | 28S ribosomal protein S7,mitochondrial,MRP-S7,S7mt,bMRP-27a,bMRP27a |
| 58 | SI | Small ribosomal subunit protein uS9m | polymer | 396 | 45909.9 | 1 | UniProt (P82933) In PDB | Homo sapiens (human) | 28S ribosomal protein S9,mitochondrial,MRP-S9,S9mt |
| 59 | SJ | Small ribosomal subunit protein uS10m | polymer | 201 | 23033.5 | 1 | UniProt (P82664) In PDB | Homo sapiens (human) | 28S ribosomal protein S10,mitochondrial,MRP-S10,S10mt |
| 60 | SK | Small ribosomal subunit protein uS11m | polymer | 194 | 20648.8 | 1 | UniProt (P82912) In PDB | Homo sapiens (human) | 28S ribosomal protein S11,mitochondrial,MRP-S11,S11mt,Cervical cancer proto-oncogene 2 protein,HCC-2 |
| 61 | SL | Small ribosomal subunit protein uS12m | polymer | 138 | 15200.9 | 1 | UniProt (O15235) In PDB | Homo sapiens (human) | 28S ribosomal protein S12,mitochondrial,MRP-S12,S12mt,MT-RPS12 |
| 62 | SN | Small ribosomal subunit protein uS14m | polymer | 128 | 15168.8 | 1 | UniProt (O60783) In PDB | Homo sapiens (human) | 28S ribosomal protein S14,mitochondrial,MRP-S14,S14mt |
| 63 | SO | Small ribosomal subunit protein uS15m | polymer | 257 | 29903.3 | 1 | UniProt (P82914) In PDB | Homo sapiens (human) | 28S ribosomal protein S15,mitochondrial,MRP-S15,S15mt |
| 64 | SP | Small ribosomal subunit protein bS16m | polymer | 137 | 15371.9 | 1 | UniProt (Q9Y3D3) In PDB | Homo sapiens (human) | 28S ribosomal protein S16,mitochondrial,MRP-S16,S16mt |
| 65 | SQ | Small ribosomal subunit protein uS17m | polymer | 130 | 14526.1 | 1 | UniProt (Q9Y2R5) In PDB | Homo sapiens (human) | 28S ribosomal protein S17,mitochondrial,MRP-S17,S17mt |
| 66 | SS | Small ribosomal subunit protein mS40 | polymer | 258 | 29440.6 | 1 | UniProt (Q9Y676) In PDB | Homo sapiens (human) | 28S ribosomal protein S18-2,mitochondrial,MRP-S18-2,28S ribosomal protein S18b,MRP-S18-b,Mrps18-b,S18mt-b,Small ribosomal subunit protein bS18b |
| 67 | ST | Small ribosomal subunit protein bS18m | polymer | 142 | 15876.8 | 1 | UniProt (Q9Y3D5) In PDB | Homo sapiens (human) | 28S ribosomal protein S18-1,mitochondrial,MRP-S18-1,28S ribosomal protein S18c,MRP-S18-c,Mrps18-c,S18mt-c,Small ribosomal subunit protein bS18c |
| 68 | SW | Small ribosomal subunit protein bS21m | polymer | 87 | 10764.7 | 1 | UniProt (P82921) In PDB | Homo sapiens (human) | 28S ribosomal protein S21,mitochondrial,MRP-S21,S21mt |
| 69 | SX | Small ribosomal subunit protein mS22 | polymer | 360 | 41337.3 | 1 | UniProt (P82650) In PDB | Homo sapiens (human) | 28S ribosomal protein S22,mitochondrial,MRP-S22,S22mt |
| 70 | SY | Small ribosomal subunit protein mS23 | polymer | 190 | 21805.7 | 1 | UniProt (Q9Y3D9) In PDB | Homo sapiens (human) | 28S ribosomal protein S23,mitochondrial,MRP-S23,S23mt |
| 71 | Sa | Small ribosomal subunit protein mS25 | polymer | 173 | 20146.4 | 1 | UniProt (P82663) In PDB | Homo sapiens (human) | 28S ribosomal protein S25,mitochondrial,MRP-S25,S25mt |
| 72 | Sb | Small ribosomal subunit protein mS26 | polymer | 205 | 24259.8 | 1 | UniProt (Q9BYN8) In PDB | Homo sapiens (human) | 28S ribosomal protein S13,mitochondrial,MRP-S13,S13mt,28S ribosomal protein S26,MRP-S26,S26mt |
| 73 | Sc | Small ribosomal subunit protein mS27 | polymer | 414 | 47669.3 | 1 | UniProt (Q92552) In PDB | Homo sapiens (human) | 28S ribosomal protein S27,mitochondrial,MRP-S27,S27mt,Mitochondrial ribosomal protein S27 |
| 74 | Sd | Small ribosomal subunit protein bS1m | polymer | 187 | 20878.8 | 1 | UniProt (Q9Y2Q9) In PDB | Homo sapiens (human) | 28S ribosomal protein S28,mitochondrial,MRP-S28,S28mt,28S ribosomal protein S35,MRP-S35,S35mt |
| 75 | Se | Small ribosomal subunit protein mS29 | polymer | 398 | 45634.4 | 1 | UniProt (P51398) In PDB | Homo sapiens (human) | 28S ribosomal protein S29,mitochondrial,MRP-S29,S29mt,Death-associated protein 3,DAP-3,Ionizing radiation resistance conferring protein |
| 76 | Sg | Small ribosomal subunit protein mS31 | polymer | 395 | 45391.5 | 1 | UniProt (Q92665) In PDB | Homo sapiens (human) | 28S ribosomal protein S31,mitochondrial,MRP-S31,S31mt,Imogen 38 |
| 77 | Si | Small ribosomal subunit protein mS33 | polymer | 106 | 12657.8 | 1 | UniProt (Q9Y291) In PDB | Homo sapiens (human) | 28S ribosomal protein S33,mitochondrial,MRP-S33,S33mt |
| 78 | Sj | Small ribosomal subunit protein mS34 | polymer | 218 | 25695.5 | 1 | UniProt (P82930) In PDB | Homo sapiens (human) | 28S ribosomal protein S34,mitochondrial,MRP-S34,S34mt |
| 79 | Sk | Small ribosomal subunit protein mS35 | polymer | 323 | 36898.3 | 1 | UniProt (P82673) In PDB | Homo sapiens (human) | 28S ribosomal protein S28,mitochondrial,MRP-S28,S28mt,28S ribosomal protein S35,MRP-S35,S35mt |
| 80 | Sm | Small ribosomal subunit protein mS37 | polymer | 118 | 13498.8 | 1 | UniProt (Q96BP2) In PDB | Homo sapiens (human) | 28S ribosomal protein S37,mitochondrial,MRP-S37,Coiled-coil-helix-coiled-coil-helix domain-containing protein 1,Nuclear protein C2360 |
| 81 | Sn | Small ribosomal subunit protein mS38 | polymer | 199 | 22395.3 | 1 | UniProt (Q9NWT8) In PDB | Homo sapiens (human) | 28S ribosomal protein S38,mitochondrial,MRP-S38,Aurora kinase A-interacting protein,AURKA-interacting protein |
| 82 | So | Small ribosomal subunit protein mS39 | polymer | 689 | 78648.5 | 1 | UniProt (Q96EY7) In PDB | Homo sapiens (human) | 28S ribosomal protein S39,mitochondrial,MRP-S39,Pentatricopeptide repeat domain-containing protein 3,Transformation-related gene 15 protein,TRG-15 |
| 83 | S1 | 12S rRNA | polymer | 954 | 306135.2 | 1 | Homo sapiens (human) | ||
| 84 | L1, S1, LB, LC, La... | MAGNESIUM ION | non-polymer | 24.3 | 145 | Chemie (MG) | |||
| 85 | S1, L1 | TIGECYCLINE | non-polymer | 587.7 | 4 | Chemie (T1C) | |||
| 86 | Lf, Lj, SR, SB, SS... | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) | |||
| 87 | Se | GUANOSINE-5'-DIPHOSPHATE | non-polymer | 443.2 | 1 | Chemie (GDP) |
Sequence modifications
SW: 1 - 87 (UniProt: P82921)
| PDB | External Database | Details |
|---|---|---|
| Arg 50 | Cys 50 | variant |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 83 |
| Total formula weight | 2882422.3 | |
| Non-Polymers* | Number of molecules | 157 |
| Total formula weight | 6775.9 | |
| All* | Total formula weight | 2889198.2 |
