9Q3Q
Cryo-EM structure of translating Escherichia coli 70S ribosome bound to mRNA, P-site QKF-peptidyl-tRNAPhe, glycyl-tRNAGly in A/T conformation, EF-Tu-GDP, and bottromycin at 2.01A resolution
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 (a) | 16S Ribosomal RNA | polymer | 1542 | 499873.4 | 1 | GenBank (1700704455) | Escherichia coli | |
| 2 | B (b) | 30S ribosomal protein S2 | polymer | 241 | 26795.7 | 1 | UniProt (J7QM75) | Escherichia coli | |
| 3 | C (c) | Small ribosomal subunit protein uS3 | polymer | 233 | 26031.3 | 1 | UniProt (B7MCS9) | Escherichia coli | |
| 4 | D (d) | Small ribosomal subunit protein uS4 | polymer | 206 | 23514.2 | 1 | UniProt (P0A7V8) | Escherichia coli | |
| 5 | E (e) | Small ribosomal subunit protein uS5 | polymer | 167 | 17629.4 | 1 | UniProt (P0A7W1) | Escherichia coli | |
| 6 | F (f) | 30S ribosomal protein S6 | polymer | 131 | 15211.1 | 1 | UniProt (C3SFQ7) | Escherichia coli | |
| 7 | G (g) | 30S ribosomal protein S7 | polymer | 156 | 17637.4 | 1 | UniProt (P02359) | Escherichia coli | Small ribosomal subunit protein uS7 |
| 8 | H (h) | Small ribosomal subunit protein uS8 | polymer | 130 | 14146.6 | 1 | UniProt (C3SR12) | Escherichia coli | |
| 9 | I (i) | Small ribosomal subunit protein uS9 | polymer | 130 | 14886.3 | 1 | UniProt (C3SRY2) | Escherichia coli | |
| 10 | J (j) | Small ribosomal subunit protein uS10 | polymer | 103 | 11755.6 | 1 | UniProt (C3SQT7) | Escherichia coli | |
| 11 | K (k) | Small ribosomal subunit protein uS11 | polymer | 129 | 13872.0 | 1 | UniProt (A7ZSI6) | Escherichia coli | 30S ribosomal protein S11 |
| 12 | L (l) | Small ribosomal subunit protein uS12 | polymer | 124 | 13814.2 | 1 | UniProt (A0A0F1AUC4) | Escherichia coli | |
| 13 | M (m) | Small ribosomal subunit protein uS13 | polymer | 118 | 13128.5 | 1 | UniProt (A0A7U9IV78) | Escherichia coli | |
| 14 | N (n) | Small ribosomal subunit protein uS14 | polymer | 101 | 11606.6 | 1 | UniProt (A0A2X1PQW4) | Escherichia coli | |
| 15 | O (o) | Small ribosomal subunit protein uS15 | polymer | 89 | 10290.8 | 1 | UniProt (C3SSQ7) | Escherichia coli | |
| 16 | P (p) | Small ribosomal subunit protein bS16 | polymer | 82 | 9207.6 | 1 | UniProt (C3SYP2) | Escherichia coli | |
| 17 | Q (q) | Small ribosomal subunit protein uS17 | polymer | 84 | 9724.5 | 1 | UniProt (C3SQY7) | Escherichia coli | |
| 18 | R (r) | Small ribosomal subunit protein bS18 | polymer | 75 | 9005.5 | 1 | UniProt (A0A0E2KXL3) | Escherichia coli | |
| 19 | S (s) | Small ribosomal subunit protein uS19 | polymer | 92 | 10455.4 | 1 | UniProt (C3SQW2) | Escherichia coli | |
| 20 | T (t) | Small ribosomal subunit protein bS20 | polymer | 87 | 9708.5 | 1 | UniProt (C3TRH7) | Escherichia coli | |
| 21 | U (u) | Small ribosomal subunit protein bS21 | polymer | 71 | 8524.0 | 1 | UniProt (A0A0E2L2J1) | Escherichia coli | |
| 22 | V (v) | dapG mRNA | polymer | 45 | 14555.7 | 1 | Escherichia coli | ||
| 23 | W (w) | A/T-site glycine tRNA | polymer | 76 | 24570.7 | 1 | Escherichia coli | ||
| 24 | X (x) | P-site phenylalanine tRNA | polymer | 76 | 24644.9 | 1 | GenBank (1850831943) | Escherichia coli | |
| 25 | Y (y) | QKF peptide | polymer | 3 | 422.5 | 1 | Escherichia coli | ||
| 26 | Z (z) | Elongation factor Tu 2 | polymer | 394 | 43370.5 | 1 | UniProt (A8A779) | Escherichia coli | EF-Tu 2 |
| 27 | AA (A) | 23S Ribosomal RNA | polymer | 2904 | 941811.6 | 1 | Escherichia coli | ||
| 28 | BA (B) | 5S Ribosomal RNA | polymer | 120 | 38814.1 | 1 | GenBank (1817378070) | Escherichia coli | |
| 29 | CA (C) | 50S ribosomal protein L2 | polymer | 273 | 29923.6 | 1 | UniProt (P60422) | Escherichia coli | Large ribosomal subunit protein uL2 |
| 30 | DA (D) | 50S ribosomal protein L3 | polymer | 209 | 22291.6 | 1 | UniProt (C3SQU2) | Escherichia coli | |
| 31 | EA (E) | Large ribosomal subunit protein uL4 | polymer | 201 | 22121.6 | 1 | UniProt (P60723) | Escherichia coli | 50S ribosomal protein L4 |
| 32 | FA (F) | Large ribosomal subunit protein uL5 | polymer | 179 | 20333.6 | 1 | UniProt (P62399) | Escherichia coli | 50S ribosomal protein L5 |
| 33 | GA (G) | Large ribosomal subunit protein uL6 | polymer | 177 | 18932.8 | 1 | UniProt (P0AG55) | Escherichia coli | 50S ribosomal protein L6 |
| 34 | HA (H) | Large ribosomal subunit protein bL9 | polymer | 149 | 15789.0 | 1 | UniProt (P0A7R1) | Escherichia coli | 50S ribosomal protein L9 |
| 35 | IA (J) | 50S ribosomal protein L11 | polymer | 142 | 14894.4 | 1 | UniProt (P0A7J7) | Escherichia coli | Large ribosomal subunit protein uL11 |
| 36 | JA (L) | Large ribosomal subunit protein uL13 | polymer | 142 | 16050.6 | 1 | UniProt (P0AA10) | Escherichia coli | 50S ribosomal protein L13 |
| 37 | KA (M) | Large ribosomal subunit protein uL14 | polymer | 123 | 13565.1 | 1 | UniProt (P0ADY3) | Escherichia coli | 50S ribosomal protein L14 |
| 38 | LA (N) | 50S ribosomal protein L15 | polymer | 144 | 14994.4 | 1 | UniProt (S5NDE9) | Escherichia coli | |
| 39 | MA (O) | Large ribosomal subunit protein uL16 | polymer | 136 | 15343.3 | 1 | UniProt (A7ZSK2) | Escherichia coli | 50S ribosomal protein L16 |
| 40 | NA (P) | Large ribosomal subunit protein bL17 | polymer | 127 | 14393.7 | 1 | UniProt (P0AG44) | Escherichia coli | 50S ribosomal protein L17 |
| 41 | OA (Q) | Large ribosomal subunit protein uL18 | polymer | 117 | 12794.7 | 1 | UniProt (P0C018) | Escherichia coli | 50S ribosomal protein L18 |
| 42 | PA (R) | Large ribosomal subunit protein bL19 | polymer | 115 | 13159.3 | 1 | UniProt (P0A7K8) | Escherichia coli | |
| 43 | QA (S) | 50S ribosomal protein L20 | polymer | 118 | 13528.0 | 1 | UniProt (B7MAS6) | Escherichia coli | |
| 44 | RA (T) | Large ribosomal subunit protein bL21 | polymer | 103 | 11586.4 | 1 | UniProt (P0AG48) | Escherichia coli | 50S ribosomal protein L21 |
| 45 | SA (U) | Large ribosomal subunit protein uL22 | polymer | 110 | 12253.4 | 1 | UniProt (P61175) | Escherichia coli | 50S ribosomal protein L22 |
| 46 | TA (V) | 50S ribosomal protein L23 | polymer | 100 | 11222.2 | 1 | UniProt (C3SQV2) | Escherichia coli | |
| 47 | UA (W) | 50S ribosomal protein L24 | polymer | 104 | 11339.3 | 1 | UniProt (C3SQZ7) | Escherichia coli | |
| 48 | VA (X) | Large ribosomal subunit protein bL25 | polymer | 94 | 10713.5 | 1 | UniProt (P68919) | Escherichia coli | 50S ribosomal protein L25 |
| 49 | WA (Y) | 50S ribosomal protein L27 | polymer | 85 | 9146.5 | 1 | UniProt (P0A7L8) | Escherichia coli | Large ribosomal subunit protein bL27 |
| 50 | XA (Z) | 50S ribosomal protein L28 | polymer | 78 | 9027.6 | 1 | UniProt (A0A1X3JA73) | Escherichia coli | |
| 51 | YA (1) | Large ribosomal subunit protein uL29 | polymer | 63 | 7286.5 | 1 | UniProt (C3SQY2) | Escherichia coli | |
| 52 | ZA (2) | 50S ribosomal protein L30 | polymer | 59 | 6554.8 | 1 | UniProt (C3SR32) | Escherichia coli | |
| 53 | AB (3) | 50S ribosomal protein L31 | polymer | 70 | 7887.1 | 1 | UniProt (P0A7M9) | Escherichia coli | Large ribosomal subunit protein bL31-A |
| 54 | BB (4) | 50S ribosomal protein L32 | polymer | 57 | 6463.4 | 1 | UniProt (C3TE02) | Escherichia coli | |
| 55 | CB (5) | 50S ribosomal protein L33 | polymer | 55 | 6388.6 | 1 | UniProt (C3SME7) | Escherichia coli | |
| 56 | DB (6) | Large ribosomal subunit protein bL34 | polymer | 46 | 5397.5 | 1 | UniProt (P0A7P5) | Escherichia coli | 50S ribosomal protein L34 |
| 57 | EB (7) | 50S ribosomal protein L35 | polymer | 65 | 7313.0 | 1 | UniProt (P0A7Q1) | Escherichia coli | Large ribosomal subunit protein bL35,Ribosomal protein A |
| 58 | FB (8) | Large ribosomal subunit protein bL36A | polymer | 38 | 4377.4 | 1 | UniProt (P0A7Q6) | Escherichia coli | 50S ribosomal protein L36,Ribosomal protein B |
| 59 | AAA, ABA, AC, AD, AE... (A, a, D, 6, 7...) | MAGNESIUM ION | non-polymer | 24.3 | 858 | Chemie (MG) PubChem (888) | |||
| 60 | ACA, ADA, AH, AI, AP... (A, a, B, f, D...) | POTASSIUM ION | non-polymer | 39.1 | 124 | Chemie (K) PubChem (813) | |||
| 61 | JI (z) | GUANOSINE-5'-DIPHOSPHATE | non-polymer | 443.2 | 1 | Chemie (GDP) | |||
| 62 | KI (z) | Bottromycin A2 | non-polymer | 823.1 | 1 | Chemie (MQH) | |||
| 63 | DNA, RMA (8, 3) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) PubChem (32051) | |||
| 64 | AOA, BOA, COA, DOA, ENA... (Y, Z, 4, 6, a...) | water | water | 18.0 | 1808 | Chemie (HOH) |
Sequence modifications
k: 1 - 129 (UniProt: A7ZSI6)
| PDB | External Database | Details |
|---|---|---|
| Ias 119 | Asn 119 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 58 |
| Total formula weight | 2260081.0 | |
| Non-Polymers* | Number of molecules | 986 |
| Total formula weight | 27098.9 | |
| All* | Total formula weight | 2287179.9 |
