7ZHG
High-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | 2 | rRNA 16S | polymer | 1497 | 487993.1 | 1 | GenBank (5457433) | Pyrococcus abyssi GE5 | |
2 | A | 30S ribosomal protein S3Ae | polymer | 199 | 22888.1 | 1 | UniProt (Q9V2K7) Pfam (PF01015) In PDB | Pyrococcus abyssi GE5 | Ribosomal protein S1e |
3 | B | 30S ribosomal protein S2 | polymer | 202 | 23026.9 | 1 | UniProt (Q9V191) Pfam (PF00318) In PDB | Pyrococcus abyssi GE5 | |
4 | C | Zn-ribbon RNA-binding protein involved in translation | polymer | 63 | 7163.4 | 1 | UniProt (G8ZFK7) Pfam (PF07754) In PDB | Pyrococcus abyssi GE5 | |
5 | D | 30S ribosomal protein S4 | polymer | 180 | 21381.9 | 1 | UniProt (P61992) Pfam (PF01479) In PDB | Pyrococcus abyssi GE5 | |
6 | E | 30S ribosomal protein S4e | polymer | 243 | 28246.1 | 1 | UniProt (Q9V1U8) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) In PDB | Pyrococcus abyssi GE5 | |
7 | F | 30S ribosomal protein S5 | polymer | 236 | 26523.9 | 1 | UniProt (Q9V1V5) Pfam (PF00333) Pfam (PF03719) In PDB | Pyrococcus abyssi GE5 | |
8 | G | 30S ribosomal protein S6e | polymer | 125 | 14029.5 | 1 | UniProt (Q9UYS3) Pfam (PF01092) In PDB | Pyrococcus abyssi GE5 | |
9 | H | 30S ribosomal protein S7 | polymer | 215 | 24662.8 | 1 | UniProt (Q9V109) Pfam (PF00177) In PDB | Pyrococcus abyssi GE5 | |
10 | I | 30S ribosomal protein S8 | polymer | 130 | 14772.2 | 1 | UniProt (Q9V1V0) Pfam (PF00410) In PDB | Pyrococcus abyssi GE5 | |
11 | J | 30S ribosomal protein S8e | polymer | 127 | 14293.7 | 1 | UniProt (Q9UZL4) Pfam (PF01201) In PDB | Pyrococcus abyssi GE5 | |
12 | K | 30S ribosomal protein S9 | polymer | 135 | 15293.9 | 1 | UniProt (Q9V195) Pfam (PF00380) In PDB | Pyrococcus abyssi GE5 | |
13 | L | 30S ribosomal protein S10 | polymer | 102 | 11795.8 | 1 | UniProt (Q9V0V6) Pfam (PF00338) In PDB | Pyrococcus abyssi GE5 | |
14 | M | 30S ribosomal protein S11 | polymer | 137 | 14773.0 | 1 | UniProt (P62010) Pfam (PF00411) In PDB | Pyrococcus abyssi GE5 | |
15 | N | 30S ribosomal protein S12 | polymer | 147 | 16477.6 | 1 | UniProt (P61994) Pfam (PF00164) In PDB | Pyrococcus abyssi GE5 | |
16 | O | 30S ribosomal protein S13 | polymer | 148 | 16992.9 | 1 | UniProt (Q9V1A0) Pfam (PF00416) In PDB | Pyrococcus abyssi GE5 | |
17 | P | 30S ribosomal protein S14 type Z | polymer | 56 | 6644.1 | 1 | UniProt (P62012) Pfam (PF00253) In PDB | Pyrococcus abyssi GE5 | |
18 | Q | 30S ribosomal protein S15 | polymer | 158 | 18697.1 | 1 | UniProt (Q9V2K9) Pfam (PF08069) Pfam (PF00312) In PDB | Pyrococcus abyssi GE5 | |
19 | R | 30S ribosomal protein S17 | polymer | 113 | 13364.6 | 1 | UniProt (Q9V1U5) Pfam (PF00366) In PDB | Pyrococcus abyssi GE5 | |
20 | S | 30S ribosomal protein S17e | polymer | 67 | 8059.5 | 1 | UniProt (Q9V0G0) Pfam (PF00833) In PDB | Pyrococcus abyssi GE5 | |
21 | T | 30S ribosomal protein S19 | polymer | 132 | 15307.3 | 1 | UniProt (Q9V1T9) Pfam (PF00203) In PDB | Pyrococcus abyssi GE5 | |
22 | U | 30S ribosomal protein S19e | polymer | 150 | 17422.3 | 1 | UniProt (Q9V0G8) Pfam (PF01090) In PDB | Pyrococcus abyssi GE5 | |
23 | V | 30S ribosomal protein S24e | polymer | 99 | 11798.6 | 1 | UniProt (Q9UY20) Pfam (PF01282) In PDB | Pyrococcus abyssi GE5 | |
24 | W | 30S ribosomal protein S27e | polymer | 65 | 7186.6 | 1 | UniProt (Q9UXZ3) Pfam (PF01667) In PDB | Pyrococcus abyssi GE5 | |
25 | X | 30S ribosomal protein S28e | polymer | 71 | 8102.3 | 1 | UniProt (P61029) Pfam (PF01200) In PDB | Pyrococcus abyssi GE5 | |
26 | Y | 30S ribosomal protein S27ae | polymer | 51 | 5992.2 | 1 | UniProt (P61238) Pfam (PF01599) In PDB | Pyrococcus abyssi GE5 | |
27 | Z | 30S ribosomal protein S3 | polymer | 210 | 23472.3 | 1 | UniProt (Q9V1U1) Pfam (PF07650) Pfam (PF00189) In PDB | Pyrococcus abyssi GE5 | |
28 | 0 | 50S ribosomal protein L41e | polymer | 36 | 4910.2 | 1 | UniProt (Q8U232) In PDB | Pyrococcus abyssi GE5 | Large ribosomal subunit protein eL41 |
29 | 3 | 50S ribosomal protein L7Ae | polymer | 123 | 13442.7 | 1 | UniProt (P62008) Pfam (PF01248) In PDB | Pyrococcus abyssi GE5 | Ribosomal protein L8e |
30 | 5 | mRNA | polymer | 17 | 5509.3 | 1 | Pyrococcus abyssi GE5 | ||
31 | 4 | Met-tRNAiMet | polymer | 77 | 24833.9 | 1 | GenBank (1334604293) | Pyrococcus abyssi GE5 | |
32 | 2, F, K, M, 5... | MAGNESIUM ION | non-polymer | 24.3 | 90 | Chemie (MG) | |||
33 | C, F, P, R, W | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) | |||
34 | water | water | 18.0 | 2083 | Chemie (HOH) |
Sequence modifications
2: 13 - 1509 (GenBank: 5457433)
4: 1 - 76 (GenBank: 1334604293)
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 0 | - | engineered mutation |
U 72 | A 3301532 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 31 |
Total formula weight | 945057.8 | |
Non-Polymers* | Number of molecules | 96 |
Total formula weight | 2579.9 | |
All* | Total formula weight | 947637.7 |