9YDD
Eukaryotic 80S ribosome with A/A, P/P tRNAs from uL16 P-site loop mutants in bypass condition
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 | A (A) | 25S RNA | polymer | 3396 | 1097454.8 | 1 | GenBank (831416132) | Saccharomyces cerevisiae S288C | |
| 2 | B (B) | 5S RNA | polymer | 121 | 38951.1 | 1 | GenBank (1329886537) | Saccharomyces cerevisiae S288C | |
| 3 | C (C) | 8S RNA | polymer | 158 | 50682.9 | 1 | GenBank (1489318609) | Saccharomyces cerevisiae S288C | |
| 4 | D (D) | messenger RNA | polymer | 10 | 3217.0 | 1 | Saccharomyces cerevisiae S288C | ||
| 5 | E (E) | 18S rRNA | polymer | 1800 | 579761.9 | 1 | GenBank (831416138) | Saccharomyces cerevisiae S288C | |
| 6 | F (LD) | 60S ribosomal protein L2-A | polymer | 254 | 27463.6 | 1 | UniProt (P0CX45) | Saccharomyces cerevisiae S288C | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
| 7 | G (LE) | 60S ribosomal protein L3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 8 | H (LF) | 60S ribosomal protein L4-A | polymer | 362 | 39159.1 | 1 | UniProt (P10664) | Saccharomyces cerevisiae S288C | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
| 9 | I (LG) | 60S ribosomal protein L5 | polymer | 297 | 33764.8 | 1 | UniProt (P26321) | Saccharomyces cerevisiae S288C | L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3 |
| 10 | J (LH) | Large ribosomal subunit protein eL6B | polymer | 176 | 20024.5 | 1 | UniProt (P05739) | Saccharomyces cerevisiae S288C | 60S ribosomal protein L6-B,L17,RP18,YL16 |
| 11 | K (LI) | 60S ribosomal protein L7-A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) | Saccharomyces cerevisiae S288C | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 12 | L (LJ) | 60S ribosomal protein L8-A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) | Saccharomyces cerevisiae S288C | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
| 13 | M (LK) | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) | Saccharomyces cerevisiae S288C | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
| 14 | N (LL) | Large ribosomal subunit protein uL16 | polymer | 210 | 24263.1 | 1 | UniProt (P41805) | Saccharomyces cerevisiae S288C | 60S ribosomal protein L10,L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
| 15 | O (LM) | Large ribosomal subunit protein uL5B | polymer | 174 | 19785.7 | 1 | UniProt (Q3E757) | Saccharomyces cerevisiae S288C | 60S ribosomal protein L11-B,L16,RP39,YL22 |
| 16 | P (LN) | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL13-A |
| 17 | Q (LO) | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL14-A |
| 18 | R (LP) | 60S ribosomal protein L15-A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) | Saccharomyces cerevisiae S288C | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
| 19 | S (LQ) | 60S ribosomal protein L16-A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) | Saccharomyces cerevisiae S288C | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
| 20 | T (LR) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) | Saccharomyces cerevisiae S288C | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 21 | U (LS) | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL18-A,RP28 |
| 22 | V (LT) | 60S ribosomal protein L19-A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) | Saccharomyces cerevisiae S288C | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
| 23 | W (LU) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) | Saccharomyces cerevisiae S288C | L18a,Large ribosomal subunit protein eL20-A |
| 24 | X (LV) | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL21-A |
| 25 | Y (LW) | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) | Saccharomyces cerevisiae S288C | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
| 26 | Z (LX) | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) | Saccharomyces cerevisiae S288C | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 27 | AA (LY) | 60S ribosomal protein L24-A | polymer | 155 | 17661.7 | 1 | UniProt (P04449) | Saccharomyces cerevisiae S288C | L30,Large ribosomal subunit protein eL24-A,RP29,YL21 |
| 28 | BA (LZ) | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 29 | CA (La) | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) | Saccharomyces cerevisiae S288C | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 30 | DA (Lb) | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL27-A |
| 31 | EA (Lc) | 60S ribosomal protein L28 | polymer | 149 | 16761.7 | 1 | UniProt (P02406) | Saccharomyces cerevisiae S288C | L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24 |
| 32 | FA (Ld) | 60S ribosomal protein L29 | polymer | 59 | 6691.9 | 1 | UniProt (P05747) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL29,YL43 |
| 33 | GA (Le) | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) | Saccharomyces cerevisiae S288C | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 34 | HA (Lf) | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) | Saccharomyces cerevisiae S288C | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 35 | IA (Lg) | 60S ribosomal protein L32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL32 |
| 36 | JA (Lh) | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) | Saccharomyces cerevisiae S288C | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 37 | KA (Li) | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL34-A |
| 38 | LA (Lj) | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein uL29-A |
| 39 | MA (Lk) | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) | Saccharomyces cerevisiae S288C | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 40 | NA (Ll) | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) | Saccharomyces cerevisiae S288C | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 41 | OA (Lm) | 60S ribosomal protein L38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL38 |
| 42 | PA (Ln) | 60S ribosomal protein L39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) | Saccharomyces cerevisiae S288C | L46,Large ribosomal subunit protein eL39,YL40 |
| 43 | QA (Lo) | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14583.1 | 1 | UniProt (P0CH08) | Saccharomyces cerevisiae S288C | |
| 44 | RA (Lp) | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 1 | UniProt (P0CX86) | Saccharomyces cerevisiae S288C | L47,YL41 |
| 45 | SA (Lq) | 60S ribosomal protein L42-A | polymer | 106 | 12246.7 | 1 | UniProt (P0CX27) | Saccharomyces cerevisiae S288C | L41,Large ribosomal subunit protein eL42-A,YL27,YP44 |
| 46 | TA (Lr) | 60S ribosomal protein L43-A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) | Saccharomyces cerevisiae S288C | L37a,Large ribosomal subunit protein eL43-A,YL35 |
| 47 | UA (SA) | 40S ribosomal protein S3 | polymer | 240 | 26542.8 | 1 | UniProt (P05750) | Saccharomyces cerevisiae S288C | RP13,YS3 |
| 48 | VA (SB) | 40S ribosomal protein S5 | polymer | 225 | 25072.6 | 1 | UniProt (P26783) | Saccharomyces cerevisiae S288C | RP14,S2,YS8 |
| 49 | WA (SC) | 40S ribosomal protein S10-A | polymer | 105 | 12757.4 | 1 | UniProt (Q08745) | Saccharomyces cerevisiae S288C | Small ribosomal subunit protein eS10-A |
| 50 | XA (SD) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 1 | UniProt (P48589) | Saccharomyces cerevisiae S288C | |
| 51 | YA (SE) | 40S ribosomal protein S15 | polymer | 142 | 16031.9 | 1 | UniProt (Q01855) | Saccharomyces cerevisiae S288C | RIG protein,RP52,S21,YS21 |
| 52 | ZA (SF) | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) | Saccharomyces cerevisiae S288C | RP61R |
| 53 | AB (SG) | 40S ribosomal protein S17-B | polymer | 136 | 15835.4 | 1 | UniProt (P14127) | Saccharomyces cerevisiae S288C | RP51B,Small ribosomal subunit protein eS17-B |
| 54 | BB (SH) | 40S ribosomal protein S18-A | polymer | 146 | 17071.6 | 1 | UniProt (P0CX55) | Saccharomyces cerevisiae S288C | Small ribosomal subunit protein uS13-A |
| 55 | CB (SI) | 40S ribosomal protein S19-A | polymer | 144 | 15942.1 | 1 | UniProt (P07280) | Saccharomyces cerevisiae S288C | RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A |
| 56 | DB (SJ) | 40S ribosomal protein S20 | polymer | 121 | 13929.0 | 1 | UniProt (P38701) | Saccharomyces cerevisiae S288C | |
| 57 | EB (SK) | 40S ribosomal protein S25-A | polymer | 108 | 12067.3 | 1 | UniProt (Q3E792) | Saccharomyces cerevisiae S288C | RP45,S31,YS23 |
| 58 | FB (SL) | 40S ribosomal protein S28-A | polymer | 67 | 7605.8 | 1 | UniProt (Q3E7X9) | Saccharomyces cerevisiae S288C | S33,Small ribosomal subunit protein eS28-A,YS27 |
| 59 | GB (SM) | 40S ribosomal protein S29-A | polymer | 56 | 6675.7 | 1 | UniProt (P41057) | Saccharomyces cerevisiae S288C | S36,YS29 |
| 60 | HB (SN) | Ubiquitin-40S ribosomal protein S31 | polymer | 152 | 17254.2 | 1 | UniProt (P05759) | Saccharomyces cerevisiae S288C | |
| 61 | IB (SO) | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 319 | 34841.2 | 1 | UniProt (P38011) | Saccharomyces cerevisiae S288C | Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1 |
| 62 | JB (SP) | 40S ribosomal protein S0-A | polymer | 252 | 28051.3 | 1 | UniProt (P32905) | Saccharomyces cerevisiae S288C | Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A |
| 63 | KB (SQ) | Small ribosomal subunit protein eS1A | polymer | 255 | 28798.5 | 1 | UniProt (P33442) | Saccharomyces cerevisiae S288C | 40S ribosomal protein S1-A,RP10A |
| 64 | LB (SR) | 40S ribosomal protein S2 | polymer | 254 | 27490.8 | 1 | UniProt (P25443) | Saccharomyces cerevisiae S288C | Omnipotent suppressor protein SUP44,RP12,S4,YS5 |
| 65 | MB (SS) | 40S ribosomal protein S4-A | polymer | 261 | 29469.3 | 1 | UniProt (P0CX35) | Saccharomyces cerevisiae S288C | RP5,S7,YS6 |
| 66 | NB (ST) | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 1 | UniProt (P0CX37) | Saccharomyces cerevisiae S288C | RP9,S10,YS4 |
| 67 | OB (SU) | 40S ribosomal protein S7-A | polymer | 190 | 21658.2 | 1 | UniProt (P26786) | Saccharomyces cerevisiae S288C | RP30,RP40 |
| 68 | PB (SV) | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 1 | UniProt (P0CX39) | Saccharomyces cerevisiae S288C | RP19,S14,YS9 |
| 69 | QB (SW) | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) | Saccharomyces cerevisiae S288C | RP21,S13,YP28,YS11 |
| 70 | RB (SX) | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 1 | UniProt (P0CX47) | Saccharomyces cerevisiae S288C | RP41,S18,YS12 |
| 71 | SB (SY) | 40S ribosomal protein S13 | polymer | 151 | 17059.9 | 1 | UniProt (P05756) | Saccharomyces cerevisiae S288C | S27a,Small ribosomal subunit protein uS15,YS15 |
| 72 | TB (SZ) | 40S ribosomal protein S14-B | polymer | 138 | 14675.8 | 1 | UniProt (P39516) | Saccharomyces cerevisiae S288C | RP59B,Small ribosomal subunit protein uS11-B |
| 73 | UB (Sa) | 40S ribosomal protein S21-A | polymer | 87 | 9758.8 | 1 | UniProt (P0C0V8) | Saccharomyces cerevisiae S288C | S26,Small ribosomal subunit protein eS21-A,YS25 |
| 74 | VB (Sb) | 40S ribosomal protein S22-A | polymer | 130 | 14650.1 | 1 | UniProt (P0C0W1) | Saccharomyces cerevisiae S288C | RP50,S24,YP58,YS22 |
| 75 | WB (Sc) | 40S ribosomal protein S23-A | polymer | 145 | 16073.9 | 1 | UniProt (P0CX29) | Saccharomyces cerevisiae S288C | RP37,S28,YS14 |
| 76 | XB (Sd) | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) | Saccharomyces cerevisiae S288C | RP50 |
| 77 | YB (Se) | Small ribosomal subunit protein eS26B | polymer | 119 | 13480.9 | 1 | UniProt (P39939) | Saccharomyces cerevisiae S288C | 40S ribosomal protein S26-B |
| 78 | ZB (Sf) | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) | Saccharomyces cerevisiae S288C | RP61,Small ribosomal subunit protein eS27-A,YS20 |
| 79 | AC (Sg) | 40S ribosomal protein S30-A | polymer | 63 | 7137.5 | 1 | UniProt (P0CX33) | Saccharomyces cerevisiae S288C | Small ribosomal subunit protein eS30-A |
| 80 | BC (m) | A site tRNA | polymer | 76 | 24378.4 | 1 | Saccharomyces cerevisiae S288C | ||
| 81 | CC (n) | P site tRNA | polymer | 75 | 24222.5 | 1 | GenBank (176433) | Saccharomyces cerevisiae S288C | |
| 82 | DC (A) | 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione | non-polymer | 281.3 | 1 | Chemie (3HE) PubChem (6197) |
Sequence modifications
A: 1 - 3396 (GenBank: 831416132)
LL: 1 - 221 (UniProt: P41805)
n: 1 - 76 (GenBank: 176433)
| PDB | External Database | Details |
|---|---|---|
| U 493 | G 3744 | conflict |
| PDB | External Database | Details |
|---|---|---|
| - | Met 102 | deletion |
| - | Leu 103 | deletion |
| - | Ser 104 | deletion |
| - | Cys 105 | deletion |
| - | Ala 106 | deletion |
| - | Gly 107 | deletion |
| - | Ala 108 | deletion |
| - | Asp 109 | deletion |
| - | Arg 110 | deletion |
| - | Leu 111 | deletion |
| - | Gln 112 | deletion |
| PDB | External Database | Details |
|---|---|---|
| A 10 | G 10 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 81 |
| Total formula weight | 3156601.4 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 281.3 | |
| All* | Total formula weight | 3156882.7 |
