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) | |||
| 85 | AG, AH, AI, AJ, AK... (L5, S2, Ln, L7, Pt...) | MAGNESIUM ION | non-polymer | 24.3 | 225 | Chemie (MG) | |||
| 86 | AM, BM, CM, DM, EM... (L5, S2, L8, La) | SODIUM ION | non-polymer | 23.0 | 35 | Chemie (NA) | |||
| 87 | DN, EN, NM, OM, PM... (L5, L8, S2, LN) | SPERMIDINE | non-polymer | 145.2 | 19 | Chemie (SPD) | |||
| 88 | AN, BN, CN, FN, WS... (L5, S2) | 1,4-DIAMINOBUTANE | non-polymer | 88.2 | 9 | Chemie (PUT) | |||
| 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) | |||
| 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 |
