8K82
Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA
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 | C2 | 18S rRNA | polymer | 1800 | 579761.9 | 1 | Saccharomyces cerevisiae | ||
| 2 | C7 | mRNA | polymer | 3 | 935.6 | 1 | Saccharomyces cerevisiae | ||
| 3 | C5 | tRNA | polymer | 75 | 24487.8 | 1 | Saccharomyces cerevisiae | ||
| 4 | C1 | 23S rRNA | polymer | 3396 | 1097493.9 | 1 | GenBank (834774822) | Saccharomyces cerevisiae (baker's yeast) | |
| 5 | C4 | 5S rRNA | polymer | 121 | 38951.1 | 1 | GenBank (1039024045) | Saccharomyces cerevisiae (baker's yeast) | 5S rRNA |
| 6 | C3 | 5.8S rRNA | polymer | 158 | 50682.9 | 1 | GenBank (1267176494) | Saccharomyces cerevisiae (baker's yeast) | |
| 7 | SA | Small ribosomal subunit protein uS2A | polymer | 252 | 28051.3 | 1 | UniProt (P32905) Pfam (PF00318) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S0-A,Nucleic acid-binding protein NAB1A |
| 8 | SB | 40S ribosomal protein S1-A | polymer | 255 | 28798.5 | 1 | UniProt (P33442) Pfam (PF01015) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP10A,Small ribosomal subunit protein eS1-A |
| 9 | SC | 40S ribosomal protein S2 | polymer | 254 | 27490.8 | 1 | UniProt (P25443) Pfam (PF00333) Pfam (PF03719) In PDB | Saccharomyces cerevisiae (baker's yeast) | Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5 |
| 10 | SD | Small ribosomal subunit protein uS3 | polymer | 240 | 26542.8 | 1 | UniProt (P05750) Pfam (PF07650) Pfam (PF00189) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S3,RP13,YS3 |
| 11 | SE | 40S ribosomal protein S4-A | polymer | 261 | 29469.3 | 1 | UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP5,S7,Small ribosomal subunit protein eS4-A,YS6 |
| 12 | SF | Small ribosomal subunit protein uS7 | polymer | 225 | 25072.6 | 1 | UniProt (P26783) Pfam (PF00177) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S5,RP14,S2,YS8 |
| 13 | SG | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 1 | UniProt (P0CX37) Pfam (PF01092) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP9,S10,Small ribosomal subunit protein eS6-A,YS4 |
| 14 | SH | 40S ribosomal protein S7-A | polymer | 190 | 21658.2 | 1 | UniProt (P26786) Pfam (PF01251) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP30,RP40,Small ribosomal subunit protein eS7-A |
| 15 | SI | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 1 | UniProt (P0CX39) Pfam (PF01201) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP19,S14,Small ribosomal subunit protein eS8-A,YS9 |
| 16 | SJ | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11 |
| 17 | SK | Small ribosomal subunit protein eS10A | polymer | 105 | 12757.4 | 1 | UniProt (Q08745) Pfam (PF03501) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S10-A |
| 18 | SL | Small ribosomal subunit protein uS17A | polymer | 156 | 17785.9 | 1 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S11-A,RP41,S18,YS12 |
| 19 | SM | Small ribosomal subunit protein eS12 | polymer | 143 | 15488.6 | 1 | UniProt (P48589) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S12 |
| 20 | SN | 40S ribosomal protein S13 | polymer | 151 | 17059.9 | 1 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) In PDB | Saccharomyces cerevisiae (baker's yeast) | S27a,Small ribosomal subunit protein uS15,YS15 |
| 21 | SO | 40S ribosomal protein S14-A | polymer | 137 | 14562.7 | 1 | UniProt (P06367) Pfam (PF00411) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP59A,Small ribosomal subunit protein uS11-A |
| 22 | SP | Small ribosomal subunit protein uS19 | polymer | 142 | 16031.9 | 1 | UniProt (Q01855) Pfam (PF00203) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S15,RIG protein,RP52,S21,YS21 |
| 23 | SQ | Small ribosomal subunit protein uS9A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S16-A,RP61R |
| 24 | SR | Small ribosomal subunit protein eS17A | polymer | 136 | 15820.4 | 1 | UniProt (P02407) Pfam (PF00833) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S17-A,RP51A |
| 25 | SS | Small ribosomal subunit protein uS13A | polymer | 146 | 17071.6 | 1 | UniProt (P0CX55) Pfam (PF00416) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S18-A |
| 26 | ST | Small ribosomal subunit protein eS19A | polymer | 144 | 15942.1 | 1 | UniProt (P07280) Pfam (PF01090) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S19-A,RP55A,S16a,YP45,YS16A |
| 27 | SU | Small ribosomal subunit protein uS10 | polymer | 121 | 13929.0 | 1 | UniProt (P38701) Pfam (PF00338) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S20 |
| 28 | SV | Small ribosomal subunit protein eS21A | polymer | 87 | 9758.8 | 1 | UniProt (P0C0V8) Pfam (PF01249) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S21-A,S26,YS25 |
| 29 | SW | 40S ribosomal protein S22-A | polymer | 130 | 14650.1 | 1 | UniProt (P0C0W1) Pfam (PF00410) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22 |
| 30 | SX | 40S ribosomal protein S23-A | polymer | 145 | 16073.9 | 1 | UniProt (P0CX29) Pfam (PF00164) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP37,S28,Small ribosomal subunit protein uS12-A,YS14 |
| 31 | SY | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP50,Small ribosomal subunit protein eS24-A |
| 32 | SZ | Small ribosomal subunit protein eS25A | polymer | 108 | 12067.3 | 1 | UniProt (Q3E792) Pfam (PF03297) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S25-A,RP45,S31,YS23 |
| 33 | Sa | Small ribosomal subunit protein eS26B | polymer | 119 | 13480.9 | 1 | UniProt (P39939) Pfam (PF01283) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S26-B |
| 34 | Sb | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) Pfam (PF01667) In PDB | Saccharomyces cerevisiae (baker's yeast) | RP61,Small ribosomal subunit protein eS27-A,YS20 |
| 35 | Sc | Small ribosomal subunit protein eS28A | polymer | 67 | 7605.8 | 1 | UniProt (Q3E7X9) Pfam (PF01200) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S28-A,S33,YS27 |
| 36 | Sd | Small ribosomal subunit protein uS14A | polymer | 56 | 6675.7 | 1 | UniProt (P41057) Pfam (PF00253) In PDB | Saccharomyces cerevisiae (baker's yeast) | 40S ribosomal protein S29-A,S36,YS29 |
| 37 | Se | 40S ribosomal protein S30-A | polymer | 63 | 7137.5 | 1 | UniProt (P0CX33) Pfam (PF04758) In PDB | Saccharomyces cerevisiae (baker's yeast) | Small ribosomal subunit protein eS30-A |
| 38 | Sf | Ubiquitin-ribosomal protein eS31 fusion protein | polymer | 152 | 17254.2 | 1 | UniProt (P05759) Pfam (PF00240) Pfam (PF01599) In PDB | Saccharomyces cerevisiae (baker's yeast) | |
| 39 | Sg | Small ribosomal subunit protein RACK1 | polymer | 319 | 34841.2 | 1 | UniProt (P38011) Pfam (PF00400) In PDB | Saccharomyces cerevisiae (baker's yeast) | Guanine nucleotide-binding protein subunit beta-like protein,Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1 |
| 40 | LA | Large ribosomal subunit protein uL2A | polymer | 254 | 27463.6 | 1 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L2-A,L5,RP8,YL6 |
| 41 | LB | Large ribosomal subunit protein uL3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) Pfam (PF00297) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 42 | LC | Large ribosomal subunit protein uL4A | polymer | 362 | 39159.1 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L4-A,L2,RP2,YL2 |
| 43 | LD | Large ribosomal subunit protein uL18 | polymer | 297 | 33764.8 | 1 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L5,L1,L1a,Ribosomal 5S RNA-binding protein,YL3 |
| 44 | LE | Large ribosomal subunit protein eL6A | polymer | 176 | 20000.6 | 1 | UniProt (Q02326) Pfam (PF01159) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L6-A,L17,RP18,YL16 |
| 45 | LF | Large ribosomal subunit protein uL30A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L7-A,L6,RP11,YL8 |
| 46 | LG | Large ribosomal subunit protein eL8A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L8-A,L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5 |
| 47 | LH | Large ribosomal subunit protein uL6A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L9-A,L8,RP24,YL11 |
| 48 | LI | Large ribosomal subunit protein uL16 | polymer | 221 | 25410.5 | 1 | UniProt (P41805) Pfam (PF00252) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L10,L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
| 49 | LJ | Large ribosomal subunit protein uL5A | polymer | 174 | 19755.7 | 1 | UniProt (P0C0W9) Pfam (PF00281) Pfam (PF00673) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L11-A,L16,RP39,YL22 |
| 50 | LK | Large ribosomal subunit protein uL11A | polymer | 165 | 17850.6 | 1 | UniProt (P0CX53) Pfam (PF03946) Pfam (PF00298) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L12-A,L15,YL23 |
| 51 | LL | Large ribosomal subunit protein eL13A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L13-A |
| 52 | LM | Large ribosomal subunit protein eL14A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L14-A |
| 53 | LN | Large ribosomal subunit protein eL15A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) Pfam (PF00827) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L15-A,L13,RP15R,YL10,YP18 |
| 54 | LO | Large ribosomal subunit protein uL13A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L16-A,L13a,L21,RP22,YL15 |
| 55 | LP | Large ribosomal subunit protein uL22A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L17-A,L20A,YL17 |
| 56 | LQ | Large ribosomal subunit protein eL18A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) Pfam (PF17135) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L18-A,RP28 |
| 57 | LR | Large ribosomal subunit protein eL19A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) Pfam (PF01280) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L19-A,L23,RP15L,RP33,YL14 |
| 58 | LS | Large ribosomal subunit protein eL20A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L20-A,L18a |
| 59 | LT | Large ribosomal subunit protein eL21A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) Pfam (PF01157) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L21-A |
| 60 | LU | Large ribosomal subunit protein eL22A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L22-A,L1c,RP4,YL31 |
| 61 | LV | Large ribosomal subunit protein uL14A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L23-A,L17a,YL32 |
| 62 | LW | Large ribosomal subunit protein eL24A | polymer | 155 | 17661.7 | 1 | UniProt (P04449) Pfam (PF01246) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L24-A,L30,RP29,YL21 |
| 63 | LX | Large ribosomal subunit protein uL23 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L25,RP16L,YL25,YP42' |
| 64 | LY | Large ribosomal subunit protein uL24A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L26-A,L33,YL33 |
| 65 | LZ | Large ribosomal subunit protein eL27A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L27-A |
| 66 | La | Large ribosomal subunit protein uL15 | polymer | 149 | 16761.7 | 1 | UniProt (P02406) Pfam (PF00828) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L28,L27a,L29,RP44,RP62,YL24 |
| 67 | Lb | Large ribosomal subunit protein eL29 | polymer | 59 | 6691.9 | 1 | UniProt (P05747) Pfam (PF01779) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L29,YL43 |
| 68 | Lc | Large ribosomal subunit protein eL30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L30,L32,RP73,YL38 |
| 69 | Ld | Large ribosomal subunit protein eL31A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L31-A,L34,YL28 |
| 70 | Le | Large ribosomal subunit protein eL32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) Pfam (PF01655) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L32 |
| 71 | Lf | Large ribosomal subunit protein eL33A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L33-A,L37,RP47,YL37 |
| 72 | Lg | Large ribosomal subunit protein eL34A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L34-A |
| 73 | Lh | Large ribosomal subunit protein uL29A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L35-A |
| 74 | Li | Large ribosomal subunit protein eL36A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L36-A,L39,YL39 |
| 75 | Lj | Large ribosomal subunit protein eL37A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L37-A,L43,YL35,YP55 |
| 76 | Lk | Large ribosomal subunit protein eL38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) Pfam (PF01781) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L38 |
| 77 | Ll | Large ribosomal subunit protein eL39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) Pfam (PF00832) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L39,L46,YL40 |
| 78 | Lm | Ubiquitin-ribosomal protein eL40A fusion protein | polymer | 128 | 14583.1 | 1 | UniProt (P0CH08) Pfam (PF00240) Pfam (PF01020) In PDB | Saccharomyces cerevisiae (baker's yeast) | |
| 79 | Ln, L2 | Large ribosomal subunit protein eL41A | polymer | 25 | 3354.2 | 2 | UniProt (P0CX86) Pfam (PF05162) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L41-A,L47,YL41 |
| 80 | Lo | Large ribosomal subunit protein eL42A | polymer | 106 | 12246.7 | 1 | UniProt (P0CX27) Pfam (PF00935) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L42-A,L41,YL27,YP44 |
| 81 | Lp | Large ribosomal subunit protein eL43A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) Pfam (PF01780) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L43-A,L37a,YL35 |
| 82 | L1 | Large ribosomal subunit protein uL1A | polymer | 217 | 24524.8 | 1 | UniProt (P0CX43) Pfam (PF00687) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S ribosomal protein L1-A,L10a |
| 83 | P0 | Large ribosomal subunit protein uL10 | polymer | 312 | 33749.1 | 1 | UniProt (P05317) Pfam (PF00466) Pfam (PF17777) Pfam (PF00428) In PDB | Saccharomyces cerevisiae (baker's yeast) | 60S acidic ribosomal protein P0,A0,L10e |
| 84 | CN | General negative regulator of transcription subunit 5 | polymer | 560 | 65948.5 | 1 | UniProt (Q12514) Pfam (PF04065) Pfam (PF04153) In PDB | Saccharomyces cerevisiae (baker's yeast) | |
| 85 | C2, C1, C4, C3, C5 | MAGNESIUM ION | non-polymer | 24.3 | 316 | Chemie (MG) | |||
| 86 | C1, C2 | TIGECYCLINE | non-polymer | 587.7 | 6 | Chemie (T1C) | |||
| 87 | C1 | SPERMIDINE | non-polymer | 145.2 | 1 | Chemie (SPD) | |||
| 88 | Lp, Sa, Sb, Sd, Sf... | ZINC ION | non-polymer | 65.4 | 9 | Chemie (ZN) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 85 |
| Total formula weight | 3276638.6 | |
| Non-Polymers* | Number of molecules | 332 |
| Total formula weight | 11940.3 | |
| All* | Total formula weight | 3288578.9 |
