8EMM
Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates
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) | 23S rRNA | polymer | 2904 | 941811.6 | 1 | Escherichia coli | ||
| 2 | B (b) | 5S rRNA | polymer | 120 | 38790.1 | 1 | GenBank (1273279017) | Escherichia coli | |
| 3 | C (c) | 50S ribosomal protein L2 | polymer | 273 | 29923.6 | 1 | UniProt (P60422) Pfam (PF00181) Pfam (PF03947) | Escherichia coli | Large ribosomal subunit protein uL2 |
| 4 | D (d) | 50S ribosomal protein L3 | polymer | 209 | 22291.6 | 1 | UniProt (U9Y9G2) Pfam (PF00297) UniProt (by SIFTS) (P60438) | Escherichia coli | |
| 5 | E (e) | 50S ribosomal protein L4 | polymer | 201 | 22121.6 | 1 | UniProt (A0A7U9FY55) Pfam (PF00573) UniProt (by SIFTS) (P60723) | Escherichia coli | |
| 6 | F (f) | 50S ribosomal protein L5 | polymer | 179 | 20333.6 | 1 | UniProt (A0A829CFT8) Pfam (PF00281) Pfam (PF00673) UniProt (by SIFTS) (P62399) | Escherichia coli | |
| 7 | G (g) | 50S ribosomal protein L6 | polymer | 177 | 18932.8 | 1 | UniProt (A0A862ZNS7) Pfam (PF00347) UniProt (by SIFTS) (P0AG55) | Escherichia coli | |
| 8 | H (h) | 50S ribosomal protein L9 | polymer | 149 | 15789.0 | 1 | UniProt (V0YZK9) Pfam (PF01281) Pfam (PF03948) UniProt (by SIFTS) (P0A7R1) | Escherichia coli | |
| 9 | I (i) | 50S ribosomal protein L13 | polymer | 142 | 16050.6 | 1 | UniProt (S1EW51) Pfam (PF00572) UniProt (by SIFTS) (P0AA10) | Escherichia coli | |
| 10 | J (j) | 50S ribosomal protein L14 | polymer | 123 | 13565.1 | 1 | UniProt (S1NW45) Pfam (PF00238) UniProt (by SIFTS) (P0ADY3) | Escherichia coli | |
| 11 | K (k) | 50S ribosomal protein L15 | polymer | 144 | 15008.5 | 1 | UniProt (A0A037Y8L6) Pfam (PF00828) UniProt (by SIFTS) (P02413) | Escherichia coli | |
| 12 | L (l) | 50S ribosomal protein L16 | polymer | 136 | 15329.3 | 1 | UniProt (A0A7U9B8R8) Pfam (PF00252) UniProt (by SIFTS) (P0ADY7) | Escherichia coli | |
| 13 | M (m) | 50S ribosomal protein L17 | polymer | 127 | 14393.7 | 1 | UniProt (A0A1X3LC97) Pfam (PF01196) UniProt (by SIFTS) (P0AG44) | Escherichia coli | |
| 14 | N (n) | 50S ribosomal protein L18 | polymer | 117 | 12794.7 | 1 | UniProt (E3PKY8) Pfam (PF00861) UniProt (by SIFTS) (P0C018) | Escherichia coli | |
| 15 | O (o) | 50S ribosomal protein L19 | polymer | 115 | 13159.3 | 1 | UniProt (V0AJX1) Pfam (PF01245) UniProt (by SIFTS) (P0A7K6) | Escherichia coli | |
| 16 | P (p) | 50S ribosomal protein L20 | polymer | 118 | 13528.0 | 1 | UniProt (B7MAS6) Pfam (PF00453) UniProt (by SIFTS) (P0A7L3) | Escherichia coli | |
| 17 | Q (q) | Ribosomal protein L21 | polymer | 103 | 11586.4 | 1 | UniProt (A0A829CSJ4) Pfam (PF00829) UniProt (by SIFTS) (P0AG48) | Escherichia coli | |
| 18 | R (r) | 50S ribosomal protein L22 | polymer | 110 | 12253.4 | 1 | UniProt (P61175) Pfam (PF00237) | Escherichia coli | Large ribosomal subunit protein uL22 |
| 19 | S (s) | 50S ribosomal protein L23 | polymer | 100 | 11222.2 | 1 | UniProt (A0A829CFV1) Pfam (PF00276) UniProt (by SIFTS) (P0ADZ0) | Escherichia coli | |
| 20 | T (t) | 50S ribosomal protein L24 | polymer | 104 | 11339.3 | 1 | UniProt (A0A1X3KWX7) Pfam (PF00467) Pfam (PF17136) UniProt (by SIFTS) (P60624) | Escherichia coli | |
| 21 | U (u) | 50S ribosomal protein L25 | polymer | 94 | 10713.5 | 1 | UniProt (D7XH79) Pfam (PF01386) UniProt (by SIFTS) (P68919) | Escherichia coli | |
| 22 | V (v) | 50S ribosomal protein L27 | polymer | 85 | 9146.5 | 1 | UniProt (P0A7L8) Pfam (PF01016) | Escherichia coli | Large ribosomal subunit protein bL27 |
| 23 | W (w) | 50S ribosomal protein L28 | polymer | 78 | 9027.6 | 1 | UniProt (A0A1X3JA73) Pfam (PF00830) UniProt (by SIFTS) (P0A7M2) | Escherichia coli | |
| 24 | X (x) | 50S ribosomal protein L29 | polymer | 63 | 7286.5 | 1 | UniProt (D6IEL0) Pfam (PF00831) UniProt (by SIFTS) (P0A7M6) | Escherichia coli | |
| 25 | Y (y) | 50S ribosomal protein L30 | polymer | 59 | 6554.8 | 1 | UniProt (V0YKA9) Pfam (PF00327) UniProt (by SIFTS) (P0AG51) | Escherichia coli | |
| 26 | Z (z) | 50S ribosomal protein L32 | polymer | 57 | 6463.4 | 1 | UniProt (D7XI28) Pfam (PF01783) UniProt (by SIFTS) (P0A7N4) | Escherichia coli | |
| 27 | AA (0) | 50S ribosomal protein L33 | polymer | 55 | 6388.6 | 1 | UniProt (F4NQ61) Pfam (PF00471) UniProt (by SIFTS) (P0A7N9) | Escherichia coli | |
| 28 | BA (1) | 50S ribosomal protein L34 | polymer | 46 | 5397.5 | 1 | UniProt (B7MGC4) Pfam (PF00468) UniProt (by SIFTS) (P0A7P5) | Escherichia coli | |
| 29 | CA (2) | 50S ribosomal protein L35 | polymer | 65 | 7313.0 | 1 | UniProt (P0A7Q1) Pfam (PF01632) | Escherichia coli | Large ribosomal subunit protein bL35,Ribosomal protein A |
| 30 | DA (3) | 50S ribosomal protein L36 | polymer | 38 | 4377.4 | 1 | UniProt (A0A0E2L017) Pfam (PF00444) UniProt (by SIFTS) (P0A7Q6) | Escherichia coli | |
| 31 | EA (4) | 50S ribosomal protein L31 | polymer | 70 | 7887.1 | 1 | UniProt (P0A7M9) Pfam (PF01197) | Escherichia coli | Large ribosomal subunit protein bL31-A |
| 32 | FA, GA (Y, Z) | Met-NH-tRNA | polymer | 76 | 24496.6 | 2 | GenBank (1848851804) | Escherichia coli | |
| 33 | HA (A) | 16S rRNA | polymer | 1542 | 499873.4 | 1 | GenBank (1758835854) | Escherichia coli | |
| 34 | IA (B) | 30S ribosomal protein S2 | polymer | 241 | 26781.7 | 1 | UniProt (C3TPN2) Pfam (PF00318) UniProt (by SIFTS) (P0A7V0) | Escherichia coli | |
| 35 | JA (C) | 30S ribosomal protein S3 | polymer | 233 | 26031.3 | 1 | UniProt (B7MCS9) Pfam (PF07650) Pfam (PF00189) UniProt (by SIFTS) (P0A7V3) | Escherichia coli | |
| 36 | KA (D) | 30S ribosomal protein S4 | polymer | 206 | 23514.2 | 1 | UniProt (P0A7V8) Pfam (PF01479) Pfam (PF00163) | Escherichia coli | |
| 37 | LA (E) | 30S ribosomal protein S5 | polymer | 167 | 17629.4 | 1 | UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719) | Escherichia coli | |
| 38 | MA (F) | 30S ribosomal protein S6 | polymer | 135 | 15727.5 | 1 | UniProt (P02358) Pfam (PF01250) | Escherichia coli | Small ribosomal subunit protein bS6 |
| 39 | NA (G) | 30S ribosomal protein S7 | polymer | 179 | 20055.2 | 1 | UniProt (P02359) Pfam (PF00177) | Escherichia coli | Small ribosomal subunit protein uS7 |
| 40 | OA (H) | 30S ribosomal protein S8 | polymer | 130 | 14146.6 | 1 | UniProt (D7XKZ3) Pfam (PF00410) UniProt (by SIFTS) (P0A7W7) | Escherichia coli | |
| 41 | PA (I) | 30S ribosomal protein S9 | polymer | 130 | 14886.3 | 1 | UniProt (A0A1X3LT86) Pfam (PF00380) UniProt (by SIFTS) (P0A7X3) | Escherichia coli | |
| 42 | QA (J) | 30S ribosomal protein S10 | polymer | 103 | 11755.6 | 1 | UniProt (V0ANK5) Pfam (PF00338) UniProt (by SIFTS) (P0A7R5) | Escherichia coli | |
| 43 | RA (K) | 30S ribosomal protein S11 | polymer | 129 | 13872.0 | 1 | UniProt (A0A0H3PWX2) Pfam (PF00411) UniProt (by SIFTS) (P0A7R9) | Escherichia coli | |
| 44 | SA (L) | 30S ribosomal protein S12 | polymer | 124 | 13814.2 | 1 | UniProt (A0A0F1AUC4) Pfam (PF00164) UniProt (by SIFTS) (P0A7S3) | Escherichia coli | |
| 45 | TA (M) | 30S ribosomal protein S13 | polymer | 118 | 13128.5 | 1 | UniProt (A0A7U9IV78) Pfam (PF00416) UniProt (by SIFTS) (P0A7S9) | Escherichia coli | |
| 46 | UA (N) | 30S ribosomal protein S14 | polymer | 101 | 11606.6 | 1 | UniProt (U9Y6H3) Pfam (PF00253) UniProt (by SIFTS) (P0AG59) | Escherichia coli | |
| 47 | VA (O) | 30S ribosomal protein S15 | polymer | 89 | 10290.8 | 1 | UniProt (D8EB41) Pfam (PF00312) UniProt (by SIFTS) (P0ADZ4) | Escherichia coli | |
| 48 | WA (P) | 30S ribosomal protein S16 | polymer | 82 | 9207.6 | 1 | UniProt (C3SYP2) Pfam (PF00886) UniProt (by SIFTS) (P0A7T3) | Escherichia coli | |
| 49 | XA (Q) | 30S ribosomal protein S17 | polymer | 84 | 9724.5 | 1 | UniProt (A0A829A8C6) Pfam (PF00366) UniProt (by SIFTS) (P0AG63) | Escherichia coli | |
| 50 | YA (R) | 30S ribosomal protein S18 | polymer | 75 | 9005.5 | 1 | UniProt (A0A0E2KXL3) Pfam (PF01084) UniProt (by SIFTS) (P0A7T7) | Escherichia coli | |
| 51 | ZA (S) | 30S ribosomal protein S19 | polymer | 92 | 10455.4 | 1 | UniProt (S1EA57) Pfam (PF00203) UniProt (by SIFTS) (P0A7U3) | Escherichia coli | |
| 52 | AB (T) | 30S ribosomal protein S20 | polymer | 87 | 9708.5 | 1 | UniProt (C3TRH7) Pfam (PF01649) UniProt (by SIFTS) (P0A7U7) | Escherichia coli | |
| 53 | BB (U) | 30S ribosomal protein S21 | polymer | 71 | 8524.0 | 1 | UniProt (A0A0E2L2J1) Pfam (PF01165) UniProt (by SIFTS) (P68679) | Escherichia coli | |
| 54 | CB (X) | mRNA | polymer | 28 | 9099.5 | 1 | Escherichia coli | ||
| 55 | AC, AD, AE, AF, AG... (a, A, Z, b, c...) | MAGNESIUM ION | non-polymer | 24.3 | 321 | Chemie (MG) | |||
| 56 | AJ, BJ, CJ, DJ, EJ... (a, A) | SPERMIDINE | non-polymer | 145.2 | 17 | Chemie (SPD) | |||
| 57 | NJ (a) | SPERMINE | non-polymer | 202.3 | 1 | Chemie (SPM) | |||
| 58 | QJ, RJ, SJ, SK, TJ... (a, c) | POTASSIUM ION | non-polymer | 39.1 | 10 | Chemie (K) | |||
| 59 | XK, YK (3, 4) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 60 | AL, ZK (Z, Y) | METHIONINE | non-polymer | 149.2 | 2 | Chemie (MET) | |||
| 61 | CL (A) | PAROMOMYCIN | non-polymer | 615.6 | 1 | Chemie (PAR) | |||
| 62 | AP, BP, CP, DP, EP... (j, k, l, m, o...) | water | water | 18.0 | 3491 | Chemie (HOH) |
Sequence modifications
l: 1 - 136 (UniProt: A0A7U9B8R8)
K: 1 - 129 (UniProt: A0A0H3PWX2)
| PDB | External Database | Details |
|---|---|---|
| Ms6 82 | Met 82 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ias 119 | Asn 119 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 55 |
| Total formula weight | 2198611.3 | |
| Non-Polymers* | Number of molecules | 354 |
| Total formula weight | 11909.3 | |
| All* | Total formula weight | 2210520.5 |
