9YDB
Eukaryotic pre-60S ribosomes from uL16 P-site loop mutants in bypass condition. Lsg1,Nmd3 and Tif6 present
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 (z) | Cytoplasmic 60S subunit biogenesis factor REH1 | polymer | 432 | 49763.8 | 1 | UniProt (Q06709) | Saccharomyces cerevisiae S288C | REI1-homolog 1,pre-60S factor REH1 |
| 5 | E (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 |
| 6 | F (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 |
| 7 | G (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 |
| 8 | H (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 |
| 9 | I (LH) | Large ribosomal subunit protein eL6B | polymer | 176 | 20024.5 | 1 | UniProt (P05739) | Saccharomyces cerevisiae S288C | 60S ribosomal protein L6-B,L17,RP18,YL16 |
| 10 | J (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 |
| 11 | K (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 |
| 12 | L (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 |
| 13 | M (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 |
| 14 | N (LM) | Large ribosomal subunit protein uL5B | polymer | 174 | 19785.7 | 1 | UniProt (Q3E757) | Saccharomyces cerevisiae S288C | 60S ribosomal protein L11-B,L16,RP39,YL22 |
| 15 | O (LN) | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL13-A |
| 16 | P (LO) | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL14-A |
| 17 | Q (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 |
| 18 | R (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 |
| 19 | S (LR) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) | Saccharomyces cerevisiae S288C | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 20 | T (LS) | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL18-A,RP28 |
| 21 | U (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 |
| 22 | V (LU) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) | Saccharomyces cerevisiae S288C | L18a,Large ribosomal subunit protein eL20-A |
| 23 | W (LV) | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL21-A |
| 24 | X (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 |
| 25 | Y (LX) | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) | Saccharomyces cerevisiae S288C | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 26 | Z (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 |
| 27 | AA (LZ) | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 28 | BA (La) | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) | Saccharomyces cerevisiae S288C | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 29 | CA (Lb) | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL27-A |
| 30 | DA (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 |
| 31 | EA (Ld) | 60S ribosomal protein L29 | polymer | 59 | 6691.9 | 1 | UniProt (P05747) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL29,YL43 |
| 32 | FA (Le) | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) | Saccharomyces cerevisiae S288C | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 33 | GA (Lf) | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) | Saccharomyces cerevisiae S288C | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 34 | HA (Lg) | 60S ribosomal protein L32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL32 |
| 35 | IA (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 |
| 36 | JA (Li) | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL34-A |
| 37 | KA (Lj) | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein uL29-A |
| 38 | LA (Lk) | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) | Saccharomyces cerevisiae S288C | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 39 | MA (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 |
| 40 | NA (Lm) | 60S ribosomal protein L38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) | Saccharomyces cerevisiae S288C | Large ribosomal subunit protein eL38 |
| 41 | OA (Ln) | 60S ribosomal protein L39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) | Saccharomyces cerevisiae S288C | L46,Large ribosomal subunit protein eL39,YL40 |
| 42 | PA (Lo) | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14583.1 | 1 | UniProt (P0CH08) | Saccharomyces cerevisiae S288C | |
| 43 | QA (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 |
| 44 | RA (Lr) | 60S ribosomal protein L43-A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) | Saccharomyces cerevisiae S288C | L37a,Large ribosomal subunit protein eL43-A,YL35 |
| 45 | SA (X) | Eukaryotic translation initiation factor 6 | polymer | 245 | 26524.6 | 1 | UniProt (Q12522) | Saccharomyces cerevisiae S288C | eIF-6 |
| 46 | TA (W) | Large subunit GTPase 1 | polymer | 640 | 72838.4 | 1 | UniProt (P53145) | Saccharomyces cerevisiae S288C | |
| 47 | UA (V) | 60S ribosomal export protein NMD3 | polymer | 518 | 59119.0 | 1 | UniProt (P38861) | Saccharomyces cerevisiae S288C | Nonsense-mediated mRNA decay protein 3 |
| 48 | VA (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)
X: 1 - 245 (UniProt: Q12522)
V: 1 - 518 (UniProt: P38861)
| 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 |
|---|---|---|
| Phe 192 | Val 192 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Asp 379 | Tyr 379 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 47 |
| Total formula weight | 2134492.3 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 281.3 | |
| All* | Total formula weight | 2134773.6 |
