8XSX
Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2
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 | L5 | 28S rRNA | polymer | 5070 | 1640182.0 | 1 | GenBank (86475748) | Homo sapiens (human) | |
| 2 | L7 | 5S rRNA | polymer | 121 | 38998.1 | 1 | GenBank (23898) | Homo sapiens (human) | |
| 3 | L8 | 5.8S rRNA | polymer | 157 | 50449.8 | 1 | GenBank (555853) | Homo sapiens (human) | Human ribosomal DNA complete repeating unit |
| 4 | LA | 60S ribosomal protein L8 | polymer | 257 | 28088.9 | 1 | UniProt (P62917) Pfam (PF03947) Pfam (PF00181) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL2 |
| 5 | LB | 60S ribosomal protein L3 | polymer | 403 | 46211.1 | 1 | UniProt (P39023) Pfam (PF00297) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL3 |
| 6 | LC | 60S ribosomal protein L4 | polymer | 427 | 47804.6 | 1 | UniProt (P36578) Pfam (PF00573) Pfam (PF14374) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL4 |
| 7 | LD | 60S ribosomal protein L5 | polymer | 297 | 34426.8 | 1 | UniProt (P46777) Pfam (PF17144) Pfam (PF14204) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL18 |
| 8 | LE | 60S ribosomal protein L6 | polymer | 288 | 32810.2 | 1 | UniProt (Q02878) Pfam (PF03868) Pfam (PF01159) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL6 |
| 9 | LF | 60S ribosomal protein L7 | polymer | 248 | 29291.0 | 1 | UniProt (P18124) Pfam (PF08079) Pfam (PF00327) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL30 |
| 10 | LG | 60S ribosomal protein L7a | polymer | 266 | 30061.8 | 1 | UniProt (P62424) Pfam (PF01248) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL8 |
| 11 | LH | 60S ribosomal protein L9 | polymer | 192 | 21899.5 | 1 | UniProt (P32969) Pfam (PF00347) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL6 |
| 12 | LI | 60S ribosomal protein L10-like | polymer | 214 | 24570.9 | 1 | UniProt (Q96L21) Pfam (PF00252) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL16-like |
| 13 | LJ | 60S ribosomal protein L11 | polymer | 178 | 20288.5 | 1 | UniProt (P62913) Pfam (PF00281) Pfam (PF00673) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL5 |
| 14 | LK | 60S ribosomal protein L12 | polymer | 165 | 17847.6 | 1 | UniProt (P30050) Pfam (PF03946) Pfam (PF00298) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL11 |
| 15 | LL | 60S ribosomal protein L13 | polymer | 211 | 24321.7 | 1 | UniProt (P26373) Pfam (PF01294) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL13 |
| 16 | LM | 60S ribosomal protein L14 | polymer | 215 | 23485.0 | 1 | UniProt (P50914) Pfam (PF01929) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL14 |
| 17 | LN | 60S ribosomal protein L15 | polymer | 204 | 24207.3 | 1 | UniProt (P61313) Pfam (PF00827) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL15 |
| 18 | LO | 60S ribosomal protein L13a | polymer | 203 | 23633.4 | 1 | UniProt (P40429) Pfam (PF00572) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL13 |
| 19 | LP | 60S ribosomal protein L17 | polymer | 184 | 21443.2 | 1 | UniProt (P18621) Pfam (PF00237) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL22 |
| 20 | LQ | 60S ribosomal protein L18 | polymer | 188 | 21687.7 | 1 | UniProt (Q07020) Pfam (PF17135) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL18 |
| 21 | LR | 60S ribosomal protein L19 | polymer | 196 | 23535.3 | 1 | UniProt (P84098) Pfam (PF01280) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL19 |
| 22 | LS | 60S ribosomal protein L18a | polymer | 176 | 20808.5 | 1 | UniProt (Q02543) Pfam (PF01775) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL20 |
| 23 | LT | 60S ribosomal protein L21 | polymer | 160 | 18610.0 | 1 | UniProt (P46778) Pfam (PF01157) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL21 |
| 24 | LU | 60S ribosomal protein L22 | polymer | 128 | 14813.0 | 1 | UniProt (P35268) Pfam (PF01776) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL22 |
| 25 | LV | 60S ribosomal protein L23 | polymer | 140 | 14892.5 | 1 | UniProt (P62829) Pfam (PF00238) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL14 |
| 26 | LW | 60S ribosomal protein L24 | polymer | 157 | 17825.1 | 1 | UniProt (P83731) Pfam (PF01246) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL24 |
| 27 | LX | 60S ribosomal protein L23a | polymer | 156 | 17740.2 | 1 | UniProt (P62750) Pfam (PF03939) Pfam (PF00276) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL23 |
| 28 | LY | 60S ribosomal protein L26 | polymer | 145 | 17303.4 | 1 | UniProt (P61254) Pfam (PF16906) Pfam (PF00467) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL24 |
| 29 | LZ | 60S ribosomal protein L27 | polymer | 136 | 15835.8 | 1 | UniProt (P61353) Pfam (PF00467) Pfam (PF01777) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL27 |
| 30 | La | 60S ribosomal protein L27a | polymer | 148 | 16604.5 | 1 | UniProt (P46776) Pfam (PF00828) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL15 |
| 31 | Lb | 60S ribosomal protein L29 | polymer | 159 | 17804.3 | 1 | UniProt (P47914) Pfam (PF01779) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL29 |
| 32 | Lc | 60S ribosomal protein L30 | polymer | 115 | 12805.1 | 1 | UniProt (P62888) Pfam (PF01248) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL30 |
| 33 | Ld | 60S ribosomal protein L31 | polymer | 125 | 14494.9 | 1 | UniProt (P62899) Pfam (PF01198) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL31 |
| 34 | Le | 60S ribosomal protein L32 | polymer | 135 | 15898.9 | 1 | UniProt (P62910) Pfam (PF01655) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL32 |
| 35 | Lf | 60S ribosomal protein L35a | polymer | 110 | 12564.7 | 1 | UniProt (P18077) Pfam (PF01247) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL33 |
| 36 | Lg | 60S ribosomal protein L34 | polymer | 117 | 13326.1 | 1 | UniProt (P49207) Pfam (PF01199) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL34 |
| 37 | Lh | 60S ribosomal protein L35 | polymer | 123 | 14593.6 | 1 | UniProt (P42766) Pfam (PF00831) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL29 |
| 38 | Li | 60S ribosomal protein L36 | polymer | 105 | 12290.9 | 1 | UniProt (Q9Y3U8) Pfam (PF01158) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL36 |
| 39 | Lj | 60S ribosomal protein L37 | polymer | 97 | 11111.0 | 1 | UniProt (P61927) Pfam (PF01907) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL37 |
| 40 | Lk | 60S ribosomal protein L38 | polymer | 70 | 8238.9 | 1 | UniProt (P63173) Pfam (PF01781) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL38 |
| 41 | Ll | 60S ribosomal protein L39 | polymer | 51 | 6426.8 | 1 | UniProt (P62891) Pfam (PF00832) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL39 |
| 42 | Lm | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14758.4 | 1 | UniProt (P62987) Pfam (PF00240) Pfam (PF01020) In PDB | Homo sapiens (human) | CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1 |
| 43 | Ln | 60S ribosomal protein L41 | polymer | 25 | 3473.5 | 1 | UniProt (P62945) Pfam (PF05162) In PDB | Homo sapiens (human) | HG12,Large ribosomal subunit protein eL41 |
| 44 | Lo | 60S ribosomal protein L36a | polymer | 106 | 12477.0 | 1 | UniProt (P83881) Pfam (PF00935) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL42 |
| 45 | Lp | 60S ribosomal protein L37a | polymer | 92 | 10299.4 | 1 | UniProt (P61513) Pfam (PF01780) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL43 |
| 46 | Lr | 60S ribosomal protein L28 | polymer | 137 | 15784.6 | 1 | UniProt (P46779) Pfam (PF01778) In PDB | Homo sapiens (human) | Large ribosomal subunit protein eL28 |
| 47 | Ls | Large ribosomal subunit protein uL10 | polymer | 317 | 34309.4 | 1 | UniProt (P05388) Pfam (PF00466) Pfam (PF17777) Pfam (PF00428) In PDB | Homo sapiens (human) | 60S acidic ribosomal protein P0,60S ribosomal protein L10E |
| 48 | Lz | 60S ribosomal protein L10a | polymer | 217 | 24879.4 | 1 | UniProt (P62906) Pfam (PF00687) In PDB | Homo sapiens (human) | Large ribosomal subunit protein uL1 |
| 49 | S2 | 18S rRNA | polymer | 1869 | 602776.9 | 1 | GenBank (36162) | Homo sapiens (human) | Human 18S ribosomal RNA |
| 50 | SA | 40S ribosomal protein SA | polymer | 295 | 32883.9 | 1 | UniProt (P08865) Pfam (PF00318) Pfam (PF16122) In PDB | Homo sapiens (human) | 37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2 |
| 51 | SB | 40S ribosomal protein S3a | polymer | 264 | 30002.1 | 1 | UniProt (P61247) Pfam (PF01015) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1 |
| 52 | SD | 40S ribosomal protein S3 | polymer | 243 | 26729.4 | 1 | UniProt (P23396) Pfam (PF07650) Pfam (PF00189) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS3 |
| 53 | SE | 40S ribosomal protein S4, X isoform | polymer | 263 | 29654.9 | 1 | UniProt (P62701) Pfam (PF08071) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) In PDB | Homo sapiens (human) | SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4 |
| 54 | SF | 40S ribosomal protein S5 | polymer | 204 | 22913.5 | 1 | UniProt (P46782) Pfam (PF00177) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS7 |
| 55 | SH | 40S ribosomal protein S7 | polymer | 194 | 22168.9 | 1 | UniProt (P62081) Pfam (PF01251) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS7 |
| 56 | SI | 40S ribosomal protein S8 | polymer | 208 | 24263.4 | 1 | UniProt (P62241) Pfam (PF01201) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS8 |
| 57 | SK | 40S ribosomal protein S10 | polymer | 165 | 18933.8 | 1 | UniProt (P46783) Pfam (PF03501) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS10 |
| 58 | SL | 40S ribosomal protein S11 | polymer | 158 | 18468.8 | 1 | UniProt (P62280) Pfam (PF16205) Pfam (PF00366) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS17 |
| 59 | SP | 40S ribosomal protein S15 | polymer | 145 | 17076.2 | 1 | UniProt (P62841) Pfam (PF00203) In PDB | Homo sapiens (human) | RIG protein,Small ribosomal subunit protein uS19 |
| 60 | SQ | 40S ribosomal protein S16 | polymer | 146 | 16477.4 | 1 | UniProt (P62249) Pfam (PF00380) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS9 |
| 61 | SR | 40S ribosomal protein S17 | polymer | 135 | 15578.2 | 1 | UniProt (P08708) Pfam (PF00833) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS17 |
| 62 | SS | 40S ribosomal protein S18 | polymer | 152 | 17759.8 | 1 | UniProt (P62269) Pfam (PF00416) In PDB | Homo sapiens (human) | Ke-3,Ke3,Small ribosomal subunit protein uS13 |
| 63 | ST | 40S ribosomal protein S19 | polymer | 145 | 16091.6 | 1 | UniProt (P39019) Pfam (PF01090) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS19 |
| 64 | SU | 40S ribosomal protein S20 | polymer | 119 | 13398.8 | 1 | UniProt (P60866) Pfam (PF00338) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS10 |
| 65 | SV | 40S ribosomal protein S21 | polymer | 83 | 9124.4 | 1 | UniProt (P63220) Pfam (PF01249) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS21 |
| 66 | SX | 40S ribosomal protein S23 | polymer | 143 | 15844.7 | 1 | UniProt (P62266) Pfam (PF00164) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS12 |
| 67 | Sa | 40S ribosomal protein S26 | polymer | 115 | 13047.5 | 1 | UniProt (P62854) Pfam (PF01283) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS26 |
| 68 | Sc | 40S ribosomal protein S28 | polymer | 69 | 7855.1 | 1 | UniProt (P62857) Pfam (PF01200) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS28 |
| 69 | Sd | 40S ribosomal protein S29 | polymer | 56 | 6690.8 | 1 | UniProt (P62273) Pfam (PF00253) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS14 |
| 70 | Sg | Receptor of activated protein C kinase 1 | polymer | 317 | 35115.7 | 1 | UniProt (P63244) Pfam (PF00400) In PDB | Homo sapiens (human) | Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1 |
| 71 | SC | 40S ribosomal protein S2 | polymer | 293 | 31376.5 | 1 | UniProt (P15880) Pfam (PF00333) Pfam (PF03719) In PDB | Homo sapiens (human) | 40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5 |
| 72 | SG | 40S ribosomal protein S6 | polymer | 249 | 28751.9 | 1 | UniProt (P62753) Pfam (PF01092) In PDB | Homo sapiens (human) | Phosphoprotein NP33,Small ribosomal subunit protein eS6 |
| 73 | SJ | 40S ribosomal protein S9 | polymer | 194 | 22641.6 | 1 | UniProt (P46781) Pfam (PF00163) Pfam (PF01479) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS4 |
| 74 | SM | 40S ribosomal protein S12 | polymer | 132 | 14539.0 | 1 | UniProt (P25398) Pfam (PF01248) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS12 |
| 75 | SN | 40S ribosomal protein S13 | polymer | 151 | 17259.4 | 1 | UniProt (P62277) Pfam (PF08069) Pfam (PF00312) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS15 |
| 76 | SO | 40S ribosomal protein S14 | polymer | 151 | 16302.8 | 1 | UniProt (P62263) Pfam (PF00411) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS11 |
| 77 | SW | 40S ribosomal protein S15a | polymer | 130 | 14865.6 | 1 | UniProt (P62244) Pfam (PF00410) In PDB | Homo sapiens (human) | Small ribosomal subunit protein uS8 |
| 78 | SY | 40S ribosomal protein S24 | polymer | 133 | 15463.3 | 1 | UniProt (P62847) Pfam (PF01282) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS24 |
| 79 | SZ | 40S ribosomal protein S25 | polymer | 125 | 13776.2 | 1 | UniProt (P62851) Pfam (PF03297) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS25 |
| 80 | Sb | 40S ribosomal protein S27 | polymer | 84 | 9480.2 | 1 | UniProt (P42677) Pfam (PF01667) In PDB | Homo sapiens (human) | Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27 |
| 81 | Se | 40S ribosomal protein S30 | polymer | 59 | 6668.9 | 1 | UniProt (P62861) Pfam (PF04758) In PDB | Homo sapiens (human) | Small ribosomal subunit protein eS30 |
| 82 | Sf | Ubiquitin-40S ribosomal protein S27a | polymer | 156 | 18004.0 | 1 | UniProt (P62979) Pfam (PF00240) Pfam (PF01599) In PDB | Homo sapiens (human) | Ubiquitin carboxyl extension protein 80 |
| 83 | CA | Proliferation-associated protein 2G4 | polymer | 394 | 43851.9 | 1 | UniProt (Q9UQ80) Pfam (PF00557) In PDB | Homo sapiens (human) | Cell cycle protein p38-2G4 homolog,hG4-1,ErbB3-binding protein 1 |
| 84 | CB | Elongation factor 2 | polymer | 858 | 95463.2 | 1 | UniProt (P13639) Pfam (PF00009) Pfam (PF03144) Pfam (PF14492) Pfam (PF03764) Pfam (PF00679) In PDB | Homo sapiens (human) | EF-2 |
| 85 | CC | E-tRNA | polymer | 75 | 24231.5 | 1 | GenBank (174924) | Homo sapiens (human) | |
| 86 | CD | SERPINE1 mRNA-binding protein 1 | polymer | 402 | 44341.8 | 1 | UniProt (Q8NC51) Pfam (PF16174) Pfam (PF04774) In PDB | Homo sapiens (human) | PAI1 RNA-binding protein 1,PAI-RBP1,Plasminogen activator inhibitor 1 RNA-binding protein |
| 87 | L5, L8, S2, LA, LB... | MAGNESIUM ION | non-polymer | 24.3 | 259 | Chemie (MG) | |||
| 88 | L5, CC | TIGECYCLINE | non-polymer | 587.7 | 7 | Chemie (T1C) | |||
| 89 | Lg, Lj, Lm, Lo, Lp... | ZINC ION | non-polymer | 65.4 | 8 | Chemie (ZN) | |||
| 90 | CB | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) |
Sequence modifications
L5: 1 - 5070 (GenBank: 86475748)
CD: 1 - 401 (UniProt: Q8NC51)
| PDB | External Database | Details |
|---|---|---|
| C 2113 | G 115460 | conflict |
| PDB | External Database | Details |
|---|---|---|
| - | Ser 202 | deletion |
| - | Ser 203 | deletion |
| - | Phe 204 | deletion |
| - | Ser 205 | deletion |
| - | His 206 | deletion |
| - | Tyr 207 | deletion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 86 |
| Total formula weight | 4065087.5 | |
| Non-Polymers* | Number of molecules | 275 |
| Total formula weight | 11359.1 | |
| All* | Total formula weight | 4076446.6 |
