7ZAG
Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA,mRNA, aIF1A and the C-terminal domain of aIF5B.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (2) | rRNA | polymer | 1497 | 487993.1 | 1 | GenBank (5457433) | Pyrococcus abyssi GE5 | |
| 2 | B (A) | 30S ribosomal protein S3Ae | polymer | 199 | 22888.1 | 1 | UniProt (Q9V2K7) Pfam (PF01015) | Pyrococcus abyssi GE5 | Ribosomal protein S1e |
| 3 | C (B) | 30S ribosomal protein S2 | polymer | 202 | 23026.9 | 1 | UniProt (Q9V191) Pfam (PF00318) | Pyrococcus abyssi GE5 | |
| 4 | D (C) | Zn-ribbon RNA-binding protein involved in translation | polymer | 63 | 7163.4 | 1 | UniProt (G8ZFK7) Pfam (PF07754) | Pyrococcus abyssi GE5 | |
| 5 | E (D) | 30S ribosomal protein S4 | polymer | 180 | 21381.9 | 1 | UniProt (P61992) Pfam (PF00163) Pfam (PF01479) | Pyrococcus abyssi GE5 | |
| 6 | F (E) | 30S ribosomal protein S4e | polymer | 243 | 28246.1 | 1 | UniProt (Q9V1U8) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) | Pyrococcus abyssi GE5 | |
| 7 | G (F) | 30S ribosomal protein S5 | polymer | 236 | 26523.9 | 1 | UniProt (Q9V1V5) Pfam (PF00333) Pfam (PF03719) | Pyrococcus abyssi GE5 | |
| 8 | H (G) | 30S ribosomal protein S6e | polymer | 125 | 14029.5 | 1 | UniProt (Q9UYS3) Pfam (PF01092) | Pyrococcus abyssi GE5 | |
| 9 | I (H) | 30S ribosomal protein S7 | polymer | 215 | 24662.8 | 1 | UniProt (Q9V109) Pfam (PF00177) | Pyrococcus abyssi GE5 | |
| 10 | J (I) | 30S ribosomal protein S8 | polymer | 130 | 14772.2 | 1 | UniProt (Q9V1V0) Pfam (PF00410) | Pyrococcus abyssi GE5 | |
| 11 | K (J) | 30S ribosomal protein S8e | polymer | 127 | 14293.7 | 1 | UniProt (Q9UZL4) Pfam (PF01201) | Pyrococcus abyssi GE5 | |
| 12 | L (K) | 30S ribosomal protein S9 | polymer | 135 | 15293.9 | 1 | UniProt (Q9V195) Pfam (PF00380) | Pyrococcus abyssi GE5 | |
| 13 | M (L) | 30S ribosomal protein S10 | polymer | 102 | 11795.8 | 1 | UniProt (Q9V0V6) Pfam (PF00338) | Pyrococcus abyssi GE5 | |
| 14 | N (M) | 30S ribosomal protein S11 | polymer | 137 | 14773.0 | 1 | UniProt (P62010) Pfam (PF00411) | Pyrococcus abyssi GE5 | |
| 15 | O (N) | 30S ribosomal protein S12 | polymer | 147 | 16477.6 | 1 | UniProt (P61994) Pfam (PF00164) | Pyrococcus abyssi GE5 | |
| 16 | P (O) | 30S ribosomal protein S13 | polymer | 148 | 16992.9 | 1 | UniProt (Q9V1A0) Pfam (PF00416) | Pyrococcus abyssi GE5 | |
| 17 | Q (P) | 30S ribosomal protein S14 type Z | polymer | 56 | 6644.1 | 1 | UniProt (P62012) Pfam (PF00253) | Pyrococcus abyssi GE5 | |
| 18 | R (Q) | 30S ribosomal protein S15 | polymer | 158 | 18697.1 | 1 | UniProt (Q9V2K9) Pfam (PF08069) Pfam (PF00312) | Pyrococcus abyssi GE5 | |
| 19 | S (R) | 30S ribosomal protein S17 | polymer | 113 | 13364.6 | 1 | UniProt (Q9V1U5) Pfam (PF00366) | Pyrococcus abyssi GE5 | |
| 20 | T (S) | 30S ribosomal protein S17e | polymer | 67 | 8059.5 | 1 | UniProt (Q9V0G0) Pfam (PF00833) | Pyrococcus abyssi GE5 | |
| 21 | U (T) | 30S ribosomal protein S19 | polymer | 132 | 15307.3 | 1 | UniProt (Q9V1T9) Pfam (PF00203) | Pyrococcus abyssi GE5 | |
| 22 | V (U) | 30S ribosomal protein S19e | polymer | 150 | 17422.3 | 1 | UniProt (Q9V0G8) Pfam (PF01090) | Pyrococcus abyssi GE5 | |
| 23 | W (V) | 30S ribosomal protein S24e | polymer | 99 | 11798.6 | 1 | UniProt (Q9UY20) Pfam (PF01282) | Pyrococcus abyssi GE5 | |
| 24 | X (W) | 30S ribosomal protein S27e | polymer | 65 | 7186.6 | 1 | UniProt (Q9UXZ3) Pfam (PF01667) | Pyrococcus abyssi GE5 | |
| 25 | Y (X) | 30S ribosomal protein S28e | polymer | 71 | 8102.3 | 1 | UniProt (P61029) Pfam (PF01200) | Pyrococcus abyssi GE5 | |
| 26 | Z (Y) | 30S ribosomal protein S27ae | polymer | 51 | 5992.2 | 1 | UniProt (P61238) Pfam (PF01599) | Pyrococcus abyssi GE5 | |
| 27 | AA (Z) | 30S ribosomal protein S3 | polymer | 210 | 23472.3 | 1 | UniProt (Q9V1U1) Pfam (PF07650) Pfam (PF00189) | Pyrococcus abyssi GE5 | |
| 28 | BA (0) | 50S ribosomal protein L41e | polymer | 36 | 4910.2 | 1 | UniProt (Q8U232) | Pyrococcus abyssi GE5 | Large ribosomal subunit protein eL41 |
| 29 | CA (3) | 50S ribosomal protein L7Ae | polymer | 123 | 13442.7 | 1 | UniProt (P62008) Pfam (PF01248) | Pyrococcus abyssi GE5 | Ribosomal protein L8e |
| 30 | DA (5) | mRNA | polymer | 25 | 8064.8 | 1 | Pyrococcus abyssi GE5 | ||
| 31 | EA (4) | Met-tRNAiMET | polymer | 77 | 24833.9 | 1 | GenBank (1334604293) | Pyrococcus abyssi GE5 | |
| 32 | FA (6) | Translation initiation factor 1A | polymer | 134 | 15336.7 | 1 | UniProt (Q9V138) Pfam (PF01176) | Pyrococcus abyssi GE5 | aIF-1A |
| 33 | GA (7) | Translation initiation factor 5B | polymer | 619 | 69122.9 | 1 | UniProt (Q9UZK7) Pfam (PF00009) Pfam (PF03144) Pfam (PF11987) Pfam (PF14578) | Pyrococcus abyssi GE5 | |
| 34 | AB, AC, BB, BC, CB... (2, F, K, 5, 4) | MAGNESIUM ION | non-polymer | 24.3 | 62 | Chemie (MG) | |||
| 35 | NC, OC, PC, SC, TC... (C, F, P, R, W) | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) | |||
| 36 | WC (4) | METHIONINE | non-polymer | 149.2 | 1 | Chemie (MET) | |||
| 37 | AD, BD, CD, DD, ED... (H, J, K, L, M...) | water | water | 18.0 | 379 | Chemie (HOH) |
Sequence modifications
2: 13 - 1509 (GenBank: 5457433)
4: 1 - 76 (GenBank: 1334604293)
6: -20 - 0 (PDB: 7ZAG)
6: 1 - 113 (UniProt: Q9V138)
7: 1 - 20 (UniProt: Q9UZK7)
7: 21 - 598 (UniProt: Q9UZK7)
| PDB | External Database | Details |
|---|---|---|
| 4ac 17 | C 205055 | modified residue |
| 4ac 53 | C 205091 | modified residue |
| 4ac 286 | C 205324 | modified residue |
| 4ac 303 | C 205341 | modified residue |
| 4ac 319 | C 205357 | modified residue |
| 4ac 379 | C 205417 | modified residue |
| 4ac 394 | C 205432 | modified residue |
| 4ac 479 | C 205517 | modified residue |
| 4ac 511 | C 205549 | modified residue |
| 4ac 546 | C 205584 | modified residue |
| 4ac 590 | C 205628 | modified residue |
| 4ac 626 | C 205664 | modified residue |
| 4ac 636 | C 205674 | modified residue |
| 4ac 703 | C 205741 | modified residue |
| 4ac 718 | C 205756 | modified residue |
| 4ac 731 | C 205769 | modified residue |
| 4ac 751 | C 205789 | modified residue |
| 4ac 828 | C 205866 | modified residue |
| 4ac 839 | C 205877 | modified residue |
| 4ac 848 | C 205886 | modified residue |
| 4ac 851 | C 205889 | modified residue |
| 4ac 868 | C 205906 | modified residue |
| 4ac 957 | C 205995 | modified residue |
| 4ac 1028 | C 206066 | modified residue |
| 4ac 1147 | C 206185 | modified residue |
| 4ac 1184 | C 206222 | modified residue |
| 4ac 1233 | C 206271 | modified residue |
| 4ac 1239 | C 206277 | modified residue |
| 4ac 1479 | C 206517 | modified residue |
| PDB | External Database | Details |
|---|---|---|
| A 1 | C 3301604 | engineered mutation |
| U 72 | A 3301532 | engineered mutation |
6: 1 - 113 (UniProt: Q9V138)
7: 1 - 20 (UniProt: Q9UZK7)
| PDB | External Database | Details |
|---|---|---|
| Met -20 | - | initiating methionine |
| Gly -19 | - | expression tag |
| Ser -18 | - | expression tag |
| Ser -17 | - | expression tag |
| His -16 | - | expression tag |
| His -15 | - | expression tag |
| His -14 | - | expression tag |
| His -13 | - | expression tag |
| His -12 | - | expression tag |
| His -11 | - | expression tag |
| Ser -10 | - | expression tag |
| Ser -9 | - | expression tag |
| Gly -8 | - | expression tag |
| Leu -7 | - | expression tag |
| Val -6 | - | expression tag |
| Pro -5 | - | expression tag |
| Arg -4 | - | expression tag |
| Gly -3 | - | expression tag |
| Ser -2 | - | expression tag |
| His -1 | - | expression tag |
| Met 0 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 33 |
| Total formula weight | 1032072.9 | |
| Non-Polymers* | Number of molecules | 69 |
| Total formula weight | 2048.6 | |
| All* | Total formula weight | 1034121.5 |
