9SPF
CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
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 (At) | A-site-tRNA-Ile-AAT-9-1 | polymer | 77 | 24794.7 | 1 | Homo sapiens | ||
| 2 | B (Et) | E site tRNA | polymer | 75 | 24231.5 | 1 | GenBank (174924) | Homo sapiens (human) | |
| 3 | C (L5) | 28S rRNA | polymer | 5069 | 1640856.5 | 1 | Homo sapiens | ||
| 4 | D (L7) | 5S rRNA | polymer | 120 | 38691.9 | 1 | GenBank (23898) | Homo sapiens (human) | |
| 5 | E (L8) | 5.8S rRNA | polymer | 156 | 50171.7 | 1 | Homo sapiens | ||
| 6 | F (LB) | Large ribosomal subunit protein uL3 | polymer | 403 | 46224.1 | 1 | UniProt (P39023) Pfam (PF00297) | Homo sapiens (human) | 60S ribosomal protein L3,HIV-1 TAR RNA-binding protein B,TARBP-B |
| 7 | G (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 |
| 8 | H (LD) | 60S ribosomal protein L5 | polymer | 297 | 34426.8 | 1 | UniProt (P46777) Pfam (PF17144) Pfam (PF14204) | Homo sapiens (human) | Large ribosomal subunit protein uL18 |
| 9 | I (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 |
| 10 | J (LF) | Large ribosomal subunit protein uL30 | polymer | 248 | 29291.0 | 1 | UniProt (P18124) Pfam (PF08079) Pfam (PF00327) | Homo sapiens (human) | 60S ribosomal protein L7 |
| 11 | K (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 |
| 12 | L (LH) | 60S ribosomal protein L9 | polymer | 192 | 21899.5 | 1 | UniProt (P32969) Pfam (PF00347) | Homo sapiens (human) | Large ribosomal subunit protein uL6 |
| 13 | M (LI) | 60S ribosomal protein L10 | polymer | 214 | 24630.1 | 1 | UniProt (P27635) Pfam (PF00252) | Homo sapiens (human) | Laminin receptor homolog,Large ribosomal subunit protein uL16,Protein QM,Ribosomal protein L10,Tumor suppressor QM |
| 14 | N (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 |
| 15 | O (LL) | Large ribosomal subunit protein eL13 | polymer | 211 | 24321.7 | 1 | UniProt (P26373) Pfam (PF01294) | Homo sapiens (human) | 60S ribosomal protein L13,Breast basic conserved protein 1 |
| 16 | P (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 |
| 17 | Q (LN) | 60S ribosomal protein L15 | polymer | 204 | 24207.3 | 1 | UniProt (P61313) Pfam (PF00827) | Homo sapiens (human) | Large ribosomal subunit protein eL15 |
| 18 | R (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 |
| 19 | S (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 |
| 20 | T (LQ) | 60S ribosomal protein L18 | polymer | 188 | 21687.7 | 1 | UniProt (Q07020) Pfam (PF17135) | Homo sapiens (human) | Large ribosomal subunit protein eL18 |
| 21 | U (LR) | 60S ribosomal protein L19 | polymer | 196 | 23535.3 | 1 | UniProt (P84098) Pfam (PF01280) Pfam (PF25476) | Homo sapiens (human) | Large ribosomal subunit protein eL19 |
| 22 | V (LS) | 60S ribosomal protein L18a | polymer | 176 | 20808.5 | 1 | UniProt (Q02543) Pfam (PF01775) | Homo sapiens (human) | Large ribosomal subunit protein eL20 |
| 23 | W (LT) | 60S ribosomal protein L21 | polymer | 160 | 18610.0 | 1 | UniProt (P46778) Pfam (PF01157) | Homo sapiens (human) | Large ribosomal subunit protein eL21 |
| 24 | X (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 |
| 25 | Y (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 |
| 26 | Z (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 |
| 27 | AA (LX) | 60S ribosomal protein L23a | polymer | 156 | 17740.2 | 1 | UniProt (P62750) Pfam (PF03939) Pfam (PF00276) | Homo sapiens (human) | Large ribosomal subunit protein uL23 |
| 28 | BA (LY) | 60S ribosomal protein L26 | polymer | 145 | 17303.4 | 1 | UniProt (P61254) Pfam (PF16906) Pfam (PF00467) | Homo sapiens (human) | Large ribosomal subunit protein uL24 |
| 29 | CA (LZ) | 60S ribosomal protein L27 | polymer | 136 | 15835.8 | 1 | UniProt (P61353) Pfam (PF00467) Pfam (PF01777) | Homo sapiens (human) | Large ribosomal subunit protein eL27 |
| 30 | DA (La) | Large ribosomal subunit protein uL15 | polymer | 148 | 16619.5 | 1 | UniProt (P46776) Pfam (PF00828) | Homo sapiens (human) | |
| 31 | EA (Lb) | Large ribosomal subunit protein eL29 | polymer | 159 | 17817.3 | 1 | UniProt (P47914) Pfam (PF01779) | Homo sapiens (human) | 60S ribosomal protein L29,Cell surface heparin-binding protein HIP |
| 32 | FA (Lc) | 60S ribosomal protein L30 | polymer | 115 | 12805.1 | 1 | UniProt (P62888) Pfam (PF01248) | Homo sapiens (human) | Large ribosomal subunit protein eL30 |
| 33 | GA (Ld) | 60S ribosomal protein L31 | polymer | 125 | 14494.9 | 1 | UniProt (P62899) Pfam (PF01198) | Homo sapiens (human) | Large ribosomal subunit protein eL31 |
| 34 | HA (Le) | 60S ribosomal protein L32 | polymer | 135 | 15898.9 | 1 | UniProt (P62910) Pfam (PF01655) | Homo sapiens (human) | Large ribosomal subunit protein eL32 |
| 35 | IA (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 |
| 36 | JA (Lg) | 60S ribosomal protein L34 | polymer | 117 | 13326.1 | 1 | UniProt (P49207) Pfam (PF01199) | Homo sapiens (human) | Large ribosomal subunit protein eL34 |
| 37 | KA (Lh) | 60S ribosomal protein L35 | polymer | 123 | 14593.6 | 1 | UniProt (P42766) Pfam (PF00831) | Homo sapiens (human) | Large ribosomal subunit protein uL29 |
| 38 | LA (Li) | 60S ribosomal protein L36 | polymer | 105 | 12290.9 | 1 | UniProt (Q9Y3U8) Pfam (PF01158) | Homo sapiens (human) | Large ribosomal subunit protein eL36 |
| 39 | MA (Lk) | 60S ribosomal protein L38 | polymer | 70 | 8238.9 | 1 | UniProt (P63173) Pfam (PF01781) | Homo sapiens (human) | Large ribosomal subunit protein eL38 |
| 40 | NA (Ll) | 60S ribosomal protein L39 | polymer | 51 | 6426.8 | 1 | UniProt (P62891) Pfam (PF00832) | Homo sapiens (human) | Large ribosomal subunit protein eL39 |
| 41 | OA (Lm) | Ubiquitin-ribosomal protein eL40 fusion protein | polymer | 128 | 14800.5 | 1 | UniProt (P62987) Pfam (PF00240) Pfam (PF01020) | Homo sapiens (human) | CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1 |
| 42 | PA (Ln) | 60S ribosomal protein L41 | polymer | 25 | 3473.5 | 1 | UniProt (P62945) Pfam (PF05162) | Homo sapiens (human) | HG12,Large ribosomal subunit protein eL41 |
| 43 | QA (Lo) | Large ribosomal subunit protein eL42 | polymer | 106 | 12490.0 | 1 | UniProt (P83881) Pfam (PF00935) | Homo sapiens (human) | 60S ribosomal protein L36a,60S ribosomal protein L44,Cell growth-inhibiting gene 15 protein,Cell migration-inducing gene 6 protein |
| 44 | RA (Lp) | 60S ribosomal protein L37a | polymer | 92 | 10299.4 | 1 | UniProt (P61513) Pfam (PF01780) | Homo sapiens (human) | Large ribosomal subunit protein eL43 |
| 45 | SA (Lr) | 60S ribosomal protein L28 | polymer | 137 | 15784.6 | 1 | UniProt (P46779) Pfam (PF01778) | Homo sapiens (human) | Large ribosomal subunit protein eL28 |
| 46 | TA (Mr) | synthetic mRNA | polymer | 7 | 2185.4 | 1 | Homo sapiens | ||
| 47 | UA (Pt) | P-site tRNA-Arg-ACG | polymer | 76 | 24579.7 | 1 | Homo sapiens | ||
| 48 | VA (S2) | 18S rRNA | polymer | 1869 | 603566.1 | 1 | Homo sapiens | ||
| 49 | WA (SB) | 40S ribosomal protein S3a | polymer | 264 | 30002.1 | 1 | UniProt (P61247) Pfam (PF01015) | Homo sapiens (human) | Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1 |
| 50 | XA (SC) | 40S ribosomal protein S2 | polymer | 293 | 31376.5 | 1 | UniProt (P15880) Pfam (PF00333) Pfam (PF03719) | Homo sapiens (human) | 40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5 |
| 51 | YA (SD) | 40S ribosomal protein S3 | polymer | 243 | 26729.4 | 1 | UniProt (P23396) Pfam (PF07650) Pfam (PF00189) | Homo sapiens (human) | Small ribosomal subunit protein uS3 |
| 52 | ZA (SE) | Small ribosomal subunit protein eS4, X isoform | polymer | 263 | 29654.9 | 1 | UniProt (P62701) Pfam (PF08071) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) | Homo sapiens (human) | 40S ribosomal protein S4,SCR10,Single copy abundant mRNA protein |
| 53 | AB (SF) | 40S ribosomal protein S5 | polymer | 204 | 22913.5 | 1 | UniProt (P46782) Pfam (PF00177) | Homo sapiens (human) | Small ribosomal subunit protein uS7 |
| 54 | BB (SG) | 40S ribosomal protein S6 | polymer | 249 | 28751.9 | 1 | UniProt (P62753) Pfam (PF01092) | Homo sapiens (human) | Phosphoprotein NP33,Small ribosomal subunit protein eS6 |
| 55 | CB (SH) | 40S ribosomal protein S7 | polymer | 194 | 22168.9 | 1 | UniProt (P62081) Pfam (PF01251) | Homo sapiens (human) | Small ribosomal subunit protein eS7 |
| 56 | DB (SI) | 40S ribosomal protein S8 | polymer | 208 | 24263.4 | 1 | UniProt (P62241) Pfam (PF01201) | Homo sapiens (human) | Small ribosomal subunit protein eS8 |
| 57 | EB (SJ) | 40S ribosomal protein S9 | polymer | 194 | 22641.6 | 1 | UniProt (P46781) Pfam (PF00163) Pfam (PF01479) | Homo sapiens (human) | Small ribosomal subunit protein uS4 |
| 58 | FB (SK) | 40S ribosomal protein S10 | polymer | 165 | 18933.8 | 1 | UniProt (P46783) Pfam (PF03501) | Homo sapiens (human) | Small ribosomal subunit protein eS10 |
| 59 | GB (SL) | 40S ribosomal protein S11 | polymer | 158 | 18468.8 | 1 | UniProt (P62280) Pfam (PF16205) Pfam (PF00366) | Homo sapiens (human) | Small ribosomal subunit protein uS17 |
| 60 | HB (SM) | 40S ribosomal protein S12 | polymer | 132 | 14539.0 | 1 | UniProt (P25398) Pfam (PF01248) | Homo sapiens (human) | Small ribosomal subunit protein eS12 |
| 61 | IB (SN) | 40S ribosomal protein S13 | polymer | 151 | 17259.4 | 1 | UniProt (P62277) Pfam (PF08069) Pfam (PF00312) | Homo sapiens (human) | Small ribosomal subunit protein uS15 |
| 62 | JB (SO) | 40S ribosomal protein S14 | polymer | 151 | 16302.8 | 1 | UniProt (P62263) Pfam (PF00411) | Homo sapiens (human) | Small ribosomal subunit protein uS11 |
| 63 | KB (SP) | 40S ribosomal protein S15 | polymer | 145 | 17076.2 | 1 | UniProt (P62841) Pfam (PF00203) | Homo sapiens (human) | RIG protein,Small ribosomal subunit protein uS19 |
| 64 | LB (SQ) | 40S ribosomal protein S16 | polymer | 146 | 16477.4 | 1 | UniProt (P62249) Pfam (PF00380) | Homo sapiens (human) | Small ribosomal subunit protein uS9 |
| 65 | MB (SR) | 40S ribosomal protein S17 | polymer | 135 | 15578.2 | 1 | UniProt (P08708) Pfam (PF00833) | Homo sapiens (human) | Small ribosomal subunit protein eS17 |
| 66 | NB (SS) | 40S ribosomal protein S18 | polymer | 152 | 17759.8 | 1 | UniProt (P62269) Pfam (PF00416) | Homo sapiens (human) | Ke-3,Ke3,Small ribosomal subunit protein uS13 |
| 67 | OB (ST) | 40S ribosomal protein S19 | polymer | 145 | 16091.6 | 1 | UniProt (P39019) Pfam (PF01090) | Homo sapiens (human) | Small ribosomal subunit protein eS19 |
| 68 | PB (SU) | 40S ribosomal protein S20 | polymer | 119 | 13398.8 | 1 | UniProt (P60866) Pfam (PF00338) | Homo sapiens (human) | Small ribosomal subunit protein uS10 |
| 69 | QB (SV) | 40S ribosomal protein S21 | polymer | 83 | 9124.4 | 1 | UniProt (P63220) Pfam (PF01249) | Homo sapiens (human) | Small ribosomal subunit protein eS21 |
| 70 | RB (SW) | 40S ribosomal protein S15a | polymer | 130 | 14865.6 | 1 | UniProt (P62244) Pfam (PF00410) | Homo sapiens (human) | Small ribosomal subunit protein uS8 |
| 71 | SB (SY) | 40S ribosomal protein S24 | polymer | 133 | 15463.3 | 1 | UniProt (P62847) Pfam (PF01282) | Homo sapiens (human) | Small ribosomal subunit protein eS24 |
| 72 | TB (SZ) | 40S ribosomal protein S25 | polymer | 125 | 13776.2 | 1 | UniProt (P62851) Pfam (PF03297) | Homo sapiens (human) | Small ribosomal subunit protein eS25 |
| 73 | UB (Sa) | 40S ribosomal protein S26 | polymer | 115 | 13047.5 | 1 | UniProt (P62854) Pfam (PF01283) | Homo sapiens (human) | Small ribosomal subunit protein eS26 |
| 74 | VB (Sb) | 40S ribosomal protein S27 | polymer | 84 | 9480.2 | 1 | UniProt (P42677) Pfam (PF01667) | Homo sapiens (human) | Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27 |
| 75 | WB (Sc) | 40S ribosomal protein S28 | polymer | 69 | 7855.1 | 1 | UniProt (P62857) Pfam (PF01200) | Homo sapiens (human) | Small ribosomal subunit protein eS28 |
| 76 | XB (Sd) | 40S ribosomal protein S29 | polymer | 56 | 6690.8 | 1 | UniProt (P62273) Pfam (PF00253) | Homo sapiens (human) | Small ribosomal subunit protein uS14 |
| 77 | YB (Se) | Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein | polymer | 133 | 14415.7 | 1 | UniProt (P62861) Pfam (PF00240) Pfam (PF04758) | Homo sapiens (human) | FAU ubiquitin like and ribosomal protein S30 fusion |
| 78 | ZB (Sf) | Ubiquitin | polymer | 156 | 18004.0 | 1 | UniProt (P62979) Pfam (PF00240) Pfam (PF01599) | Homo sapiens (human) | |
| 79 | AC (Sg) | Receptor of activated protein C kinase 1 | polymer | 317 | 35115.7 | 1 | UniProt (P63244) Pfam (PF00400) | 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 |
| 80 | BC (LA) | Large ribosomal subunit protein uL2 | polymer | 257 | 28103.9 | 1 | UniProt (P62917) Pfam (PF00181) Pfam (PF03947) | Homo sapiens (human) | 60S ribosomal protein L8 |
| 81 | CC (SA) | Small ribosomal subunit protein uS2 | polymer | 295 | 32778.8 | 1 | UniProt (P08865) Pfam (PF00318) Pfam (PF16122) | Homo sapiens (human) | 37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,40S ribosomal protein SA,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 |
| 82 | DC (SX) | 40S ribosomal protein S23 | polymer | 143 | 15860.7 | 1 | UniProt (A0A4W2DI10) Pfam (PF00164) | Homo sapiens (human) | |
| 83 | EC (Lj) | Large ribosomal subunit protein eL37 | polymer | 97 | 11111.0 | 1 | UniProt (P61927) Pfam (PF01907) | Homo sapiens (human) | 60S ribosomal protein L37,G1.16 |
| 84 | AD, AE, AF, AO, AP... (L5, Lg, S2, SF, SL...) | POTASSIUM ION | non-polymer | 39.1 | 151 | Chemie (K) PubChem (813) | |||
| 85 | AG, AH, AI, AJ, AK... (L5, S2, Ln, L7, Pt...) | MAGNESIUM ION | non-polymer | 24.3 | 225 | Chemie (MG) PubChem (888) | |||
| 86 | AM, BM, CM, DM, EM... (L5, S2, L8, La) | SODIUM ION | non-polymer | 23.0 | 35 | Chemie (NA) PubChem (923) | |||
| 87 | DN, EN, NM, OM, PM... (L5, L8, S2, LN) | SPERMIDINE | non-polymer | 145.2 | 19 | Chemie (SPD) PubChem (1102) | |||
| 88 | AN, BN, CN, FN, WS... (L5, S2) | 1,4-DIAMINOBUTANE | non-polymer | 88.2 | 9 | Chemie (PUT) PubChem (1045) | |||
| 89 | BO, CO, ET, FO, GO... (Lg, Lm, Sa, Lo, Lp...) | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) | |||
| 90 | ZS (S2) | HYGROMYCIN B | non-polymer | 527.5 | 1 | Chemie (HYG) PubChem (16219464) PubChem (20054887) PubChem (44120020) PubChem (20054942) PubChem (23777801) PubChem (24875318) PubChem (52949613) PubChem (53315786) PubChem (57511216) PubChem (58160574) PubChem (446111) PubChem (46943429) PubChem (71571512) PubChem (53393586) PubChem (56928061) PubChem (76336793) PubChem (3068367) PubChem (176519971) PubChem (89936880) PubChem (3659) PubChem (35766) PubChem (90488914) PubChem (76971015) PubChem (76971016) PubChem (502206) PubChem (91617579) PubChem (98048103) PubChem (5460094) PubChem (124809074) PubChem (124809080) PubChem (125461707) PubChem (93974294) PubChem (129606984) PubChem (131632475) PubChem (94865124) PubChem (94865125) PubChem (96327587) PubChem (96327588) PubChem (98048102) PubChem (101828545) PubChem (134693050) PubChem (117683867) PubChem (118039329) PubChem (118318030) PubChem (13036911) PubChem (139026182) PubChem (124328800) PubChem (124433112) PubChem (124524088) PubChem (124524089) PubChem (139595130) PubChem (146027508) PubChem (124809075) PubChem (124809078) PubChem (162883455) PubChem (162883447) PubChem (162883454) PubChem (125461706) PubChem (125461708) PubChem (168314873) PubChem (129010089) PubChem (129606985) PubChem (134129613) PubChem (138107735) PubChem (138319323) PubChem (139595131) PubChem (145944872) PubChem (146027509) PubChem (146158568) PubChem (154825180) PubChem (157209529) PubChem (160508452) PubChem (160508454) PubChem (162883446) PubChem (162883448) PubChem (162883449) PubChem (162883450) PubChem (162883451) PubChem (162883452) PubChem (162883453) PubChem (168911900) PubChem (169442324) PubChem (172878373) PubChem (173721900) | |||
| 91 | AU, BU, CU, DU, EU... (Lp, Mr, Pt, S2, SN...) | water | water | 18.0 | 517 | Chemie (HOH) |
Sequence modifications
SA: 2 - 295 (UniProt: P08865)
| PDB | External Database | Details |
|---|---|---|
| Ace 2 | - | acetylation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 83 |
| Total formula weight | 3864661.2 | |
| Non-Polymers* | Number of molecules | 447 |
| Total formula weight | 16715.5 | |
| All* | Total formula weight | 3881376.7 |
