9GY4
60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map)
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 (5) | 28S rRNA | polymer | 5070 | 1640166.9 | 1 | GenBank (86475748) | Homo sapiens (human) | |
| 2 | B (7) | 5S rRNA | polymer | 121 | 38998.1 | 1 | GenBank (23898) | Homo sapiens (human) | |
| 3 | C (8) | 5.8S rRNA | polymer | 157 | 50449.8 | 1 | GenBank (555853) | Homo sapiens (human) | |
| 4 | D (B) | CDK5 regulatory subunit-associated protein 3 | polymer | 506 | 56977.4 | 1 | UniProt (Q96JB5) Pfam (PF05600) | Homo sapiens (human) | CDK5 activator-binding protein C53,LXXLL/leucine-zipper-containing ARF-binding protein,Protein HSF-27 |
| 5 | E (C) | DDRGK domain-containing protein 1 | polymer | 314 | 35663.8 | 1 | UniProt (Q96HY6) Pfam (PF09756) | Homo sapiens (human) | Dashurin,UFM1-binding and PCI domain-containing protein 1 |
| 6 | F (D) | Ubiquitin-fold modifier 1 | polymer | 85 | 9128.6 | 1 | UniProt (P61960) Pfam (PF03671) | Homo sapiens (human) | |
| 7 | G (E) | E3 UFM1-protein ligase 1 | polymer | 794 | 89722.2 | 1 | UniProt (O94874) Pfam (PF09743) Pfam (PF25870) Pfam (PF23659) Pfam (PF25041) | Homo sapiens (human) | E3 UFM1-protein transferase 1,Multiple alpha-helix protein located at ER,Novel LZAP-binding protein,Regulator of C53/LZAP and DDRGK1 |
| 8 | H (F) | E3 ubiquitin-protein ligase listerin | polymer | 1766 | 200778.7 | 1 | UniProt (O94822) Pfam (PF22999) Pfam (PF23009) Pfam (PF22958) Pfam (PF24618) | Homo sapiens (human) | RING finger protein 160,RING-type E3 ubiquitin transferase listerin,Zinc finger protein 294 |
| 9 | I (G) | tRNA | polymer | 76 | 24502.5 | 1 | GenBank (2736373571) | Homo sapiens (human) | |
| 10 | J (LB) | 60S ribosomal protein L3 | polymer | 403 | 46211.1 | 1 | UniProt (P39023) Pfam (PF00297) | Homo sapiens (human) | HIV-1 TAR RNA-binding protein B,TARBP-B,Large ribosomal subunit protein uL3 |
| 11 | K (LC) | 60S ribosomal protein L4 | polymer | 427 | 47804.6 | 1 | UniProt (P36578) Pfam (PF00573) Pfam (PF14374) | Homo sapiens (human) | 60S ribosomal protein L1,Large ribosomal subunit protein uL4 |
| 12 | L (LD) | 60S ribosomal protein L5 | polymer | 297 | 34426.8 | 1 | UniProt (P46777) Pfam (PF17144) Pfam (PF14204) | Homo sapiens (human) | Large ribosomal subunit protein uL18 |
| 13 | M (LE) | Large ribosomal subunit protein eL6 | polymer | 288 | 32810.2 | 1 | UniProt (Q02878) Pfam (PF03868) Pfam (PF01159) | Homo sapiens (human) | 60S ribosomal protein L6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107 |
| 14 | N (LF) | Large ribosomal subunit protein uL30 | polymer | 248 | 29291.0 | 1 | UniProt (P18124) Pfam (PF08079) Pfam (PF00327) | Homo sapiens (human) | 60S ribosomal protein L7 |
| 15 | O (LG) | 60S ribosomal protein L7a | polymer | 266 | 30061.8 | 1 | UniProt (P62424) Pfam (PF01248) | Homo sapiens (human) | Large ribosomal subunit protein eL8,PLA-X polypeptide,Surfeit locus protein 3 |
| 16 | P (LH) | 60S ribosomal protein L9 | polymer | 192 | 21899.5 | 1 | UniProt (P32969) Pfam (PF00347) | Homo sapiens (human) | Large ribosomal subunit protein uL6 |
| 17 | Q (LI) | Ribosomal protein uL16-like | polymer | 214 | 24552.9 | 1 | UniProt (Q96L21) Pfam (PF00252) | Homo sapiens (human) | 60S ribosomal protein L10-like,Large ribosomal subunit protein uL16-like |
| 18 | R (LJ) | 60S ribosomal protein L11 | polymer | 178 | 20288.5 | 1 | UniProt (P62913) Pfam (PF00281) Pfam (PF00673) | Homo sapiens (human) | CLL-associated antigen KW-12,Large ribosomal subunit protein uL5 |
| 19 | S (LL) | 60S ribosomal protein L13 | polymer | 211 | 24321.7 | 1 | UniProt (P26373) Pfam (PF01294) | Homo sapiens (human) | Breast basic conserved protein 1,Large ribosomal subunit protein eL13 |
| 20 | T (LM) | 60S ribosomal protein L14 | polymer | 215 | 23485.0 | 1 | UniProt (P50914) Pfam (PF01929) | Homo sapiens (human) | CAG-ISL 7,Large ribosomal subunit protein eL14 |
| 21 | U (LN) | 60S ribosomal protein L15 | polymer | 204 | 24207.3 | 1 | UniProt (P61313) Pfam (PF00827) | Homo sapiens (human) | Large ribosomal subunit protein eL15 |
| 22 | V (LO) | 60S ribosomal protein L13a | polymer | 203 | 23633.4 | 1 | UniProt (P40429) Pfam (PF00572) | Homo sapiens (human) | 23 kDa highly basic protein,Large ribosomal subunit protein uL13 |
| 23 | W (LP) | 60S ribosomal protein L17 | polymer | 184 | 21443.2 | 1 | UniProt (P18621) Pfam (PF00237) | Homo sapiens (human) | 60S ribosomal protein L23,Large ribosomal subunit protein uL22,PD-1 |
| 24 | X (LQ) | 60S ribosomal protein L18 | polymer | 188 | 21687.7 | 1 | UniProt (Q07020) Pfam (PF17135) | Homo sapiens (human) | Large ribosomal subunit protein eL18 |
| 25 | Y (LR) | 60S ribosomal protein L19 | polymer | 196 | 23535.3 | 1 | UniProt (P84098) Pfam (PF01280) Pfam (PF25476) | Homo sapiens (human) | Large ribosomal subunit protein eL19 |
| 26 | Z (LS) | 60S ribosomal protein L18a | polymer | 176 | 20808.5 | 1 | UniProt (Q02543) Pfam (PF01775) | Homo sapiens (human) | Large ribosomal subunit protein eL20 |
| 27 | AA (LT) | 60S ribosomal protein L21 | polymer | 160 | 18610.0 | 1 | UniProt (P46778) Pfam (PF01157) | Homo sapiens (human) | Large ribosomal subunit protein eL21 |
| 28 | BA (LU) | 60S ribosomal protein L22 | polymer | 128 | 14813.0 | 1 | UniProt (P35268) Pfam (PF01776) | Homo sapiens (human) | EBER-associated protein,EAP,Epstein-Barr virus small RNA-associated protein,Heparin-binding protein HBp15,Large ribosomal subunit protein eL22 |
| 29 | CA (LV) | 60S ribosomal protein L23 | polymer | 140 | 14892.5 | 1 | UniProt (P62829) Pfam (PF00238) | Homo sapiens (human) | 60S ribosomal protein L17,Large ribosomal subunit protein uL14 |
| 30 | DA (LW) | 60S ribosomal protein L24 | polymer | 157 | 17825.1 | 1 | UniProt (P83731) Pfam (PF01246) | Homo sapiens (human) | 60S ribosomal protein L30,Large ribosomal subunit protein eL24 |
| 31 | EA (LX) | 60S ribosomal protein L23a | polymer | 156 | 17740.2 | 1 | UniProt (P62750) Pfam (PF03939) Pfam (PF00276) | Homo sapiens (human) | Large ribosomal subunit protein uL23 |
| 32 | FA (LY) | 60S ribosomal protein L26 | polymer | 145 | 17303.4 | 1 | UniProt (P61254) Pfam (PF16906) Pfam (PF00467) | Homo sapiens (human) | Large ribosomal subunit protein uL24 |
| 33 | GA (LZ) | 60S ribosomal protein L27 | polymer | 136 | 15835.8 | 1 | UniProt (P61353) Pfam (PF00467) Pfam (PF01777) | Homo sapiens (human) | Large ribosomal subunit protein eL27 |
| 34 | HA (La) | 60S ribosomal protein L27a | polymer | 148 | 16604.5 | 1 | UniProt (P46776) Pfam (PF00828) | Homo sapiens (human) | Large ribosomal subunit protein uL15 |
| 35 | IA (Lb) | 60S ribosomal protein L29 | polymer | 159 | 17804.3 | 1 | UniProt (P47914) Pfam (PF01779) | Homo sapiens (human) | Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29 |
| 36 | JA (Lc) | 60S ribosomal protein L30 | polymer | 115 | 12805.1 | 1 | UniProt (P62888) Pfam (PF01248) | Homo sapiens (human) | Large ribosomal subunit protein eL30 |
| 37 | KA (Ld) | 60S ribosomal protein L31 | polymer | 125 | 14494.9 | 1 | UniProt (P62899) Pfam (PF01198) | Homo sapiens (human) | Large ribosomal subunit protein eL31 |
| 38 | LA (Le) | 60S ribosomal protein L32 | polymer | 135 | 15898.9 | 1 | UniProt (P62910) Pfam (PF01655) | Homo sapiens (human) | Large ribosomal subunit protein eL32 |
| 39 | MA (Lf) | 60S ribosomal protein L35a | polymer | 110 | 12564.7 | 1 | UniProt (P18077) Pfam (PF01247) | Homo sapiens (human) | Cell growth-inhibiting gene 33 protein,Large ribosomal subunit protein eL33 |
| 40 | NA (Lg) | 60S ribosomal protein L34 | polymer | 117 | 13326.1 | 1 | UniProt (P49207) Pfam (PF01199) | Homo sapiens (human) | Large ribosomal subunit protein eL34 |
| 41 | OA (Lh) | 60S ribosomal protein L35 | polymer | 123 | 14593.6 | 1 | UniProt (P42766) Pfam (PF00831) | Homo sapiens (human) | Large ribosomal subunit protein uL29 |
| 42 | PA (Li) | 60S ribosomal protein L36 | polymer | 105 | 12290.9 | 1 | UniProt (Q9Y3U8) Pfam (PF01158) | Homo sapiens (human) | Large ribosomal subunit protein eL36 |
| 43 | QA (Lj) | 60S ribosomal protein L37 | polymer | 97 | 11111.0 | 1 | UniProt (P61927) Pfam (PF01907) | Homo sapiens (human) | G1.16,Large ribosomal subunit protein eL37 |
| 44 | RA (Lk) | 60S ribosomal protein L38 | polymer | 70 | 8238.9 | 1 | UniProt (P63173) Pfam (PF01781) | Homo sapiens (human) | Large ribosomal subunit protein eL38 |
| 45 | SA (Ll) | 60S ribosomal protein L39 | polymer | 51 | 6426.8 | 1 | UniProt (P62891) Pfam (PF00832) | Homo sapiens (human) | Large ribosomal subunit protein eL39 |
| 46 | TA (Lm) | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14758.4 | 1 | UniProt (P62987) Pfam (PF00240) Pfam (PF01020) | Homo sapiens (human) | CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1 |
| 47 | UA (Lo) | 60S ribosomal protein L36a | polymer | 106 | 12477.0 | 1 | UniProt (P83881) Pfam (PF00935) | Homo sapiens (human) | 60S ribosomal protein L44,Cell growth-inhibiting gene 15 protein,Cell migration-inducing gene 6 protein,Large ribosomal subunit protein eL42 |
| 48 | VA (Lp) | 60S ribosomal protein L37a | polymer | 92 | 10299.4 | 1 | UniProt (P61513) Pfam (PF01780) | Homo sapiens (human) | Large ribosomal subunit protein eL43 |
| 49 | WA (Lr) | 60S ribosomal protein L28 | polymer | 137 | 15784.6 | 1 | UniProt (P46779) Pfam (PF01778) | Homo sapiens (human) | Large ribosomal subunit protein eL28 |
| 50 | XA (Lz) | 60S ribosomal protein L10a | polymer | 217 | 24879.4 | 1 | UniProt (P62906) Pfam (PF00687) | Homo sapiens (human) | CSA-19,Large ribosomal subunit protein uL1,Neural precursor cell expressed developmentally down-regulated protein 6,NEDD-6 |
| 51 | YA (Z) | Ribosome quality control complex subunit NEMF | polymer | 1076 | 123146.5 | 1 | UniProt (O60524) Pfam (PF05833) Pfam (PF05670) Pfam (PF11923) | Homo sapiens (human) | Antigen NY-CO-1,Nuclear export mediator factor,Serologically defined colon cancer antigen 1 |
| 52 | ZA (a) | 60S ribosomal protein L8 | polymer | 257 | 28088.9 | 1 | UniProt (P62917) Pfam (PF00181) Pfam (PF03947) | Homo sapiens (human) | Large ribosomal subunit protein uL2 |
| 53 | AB (s) | 60S acidic ribosomal protein P0 | polymer | 317 | 34309.4 | 1 | UniProt (P05388) Pfam (PF00466) Pfam (PF17777) Pfam (PF00428) | Homo sapiens (human) | 60S ribosomal protein L10E,Large ribosomal subunit protein uL10 |
| 54 | BB (t) | Large ribosomal subunit protein uL11 | polymer | 165 | 17847.6 | 1 | UniProt (P30050) Pfam (PF03946) Pfam (PF00298) | Homo sapiens (human) | 60S ribosomal protein L12 |
| 55 | CB (A) | Nascent chain | polymer | 7 | 613.7 | 1 | Homo sapiens (human) | ||
| 56 | AC, AD, AE, AF, AG... (5, 7, 8, LI, LP...) | MAGNESIUM ION | non-polymer | 24.3 | 219 | Chemie (MG) | |||
| 57 | NJ, PJ, QJ, RJ, SJ (Lg, Lj, Lm, Lo, Lp) | ZINC ION | non-polymer | 65.4 | 5 | Chemie (ZN) |
Sequence modifications
5: 1 - 5070 (GenBank: 86475748)
G: 1 - 76 (GenBank: 2736373571)
LI: 1 - 214 (UniProt: Q96L21)
| PDB | External Database | Details |
|---|---|---|
| C 2113 | G 115460 | conflict |
| U 4906 | C 118253 | conflict |
| A 4910 | G 118257 | conflict |
| PDB | External Database | Details |
|---|---|---|
| G 73 | A 140694 | conflict |
| C 74 | A 140693 | conflict |
| C 75 | U 140692 | conflict |
| A 76 | C 140691 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ile 87 | Met 87 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 55 |
| Total formula weight | 3172241.0 | |
| Non-Polymers* | Number of molecules | 224 |
| Total formula weight | 5649.8 | |
| All* | Total formula weight | 3177890.9 |
