9IOT
Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant
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 (0) | Large ribosomal subunit protein uL29 | polymer | 63 | 7286.5 | 1 | UniProt (P0A7M6) Pfam (PF00831) | Escherichia coli | 50S ribosomal protein L29 |
| 2 | B (1) | Large ribosomal subunit protein uL30 | polymer | 59 | 6554.8 | 1 | UniProt (P0AG51) Pfam (PF00327) | Escherichia coli | 50S ribosomal protein L30 |
| 3 | C (3) | Large ribosomal subunit protein bL32 | polymer | 57 | 6463.4 | 1 | UniProt (P0A7N4) Pfam (PF01783) | Escherichia coli | 50S ribosomal protein L32 |
| 4 | D (4) | Large ribosomal subunit protein bL33 | polymer | 55 | 6388.6 | 1 | UniProt (P0A7N9) Pfam (PF00471) | Escherichia coli | 50S ribosomal protein L33 |
| 5 | E (5) | 50S ribosomal protein L34 | polymer | 46 | 5397.5 | 1 | UniProt (P0A7P5) Pfam (PF00468) | Escherichia coli | Large ribosomal subunit protein bL34 |
| 6 | F (6) | Large ribosomal subunit protein bL35 | polymer | 65 | 7313.0 | 1 | UniProt (P0A7Q1) Pfam (PF01632) | Escherichia coli | 50S ribosomal protein L35,Ribosomal protein A |
| 7 | G (7) | 50S ribosomal protein L36 | polymer | 38 | 4377.4 | 1 | UniProt (P0A7Q6) Pfam (PF00444) | Escherichia coli | Large ribosomal subunit protein bL36-A,Ribosomal protein B |
| 8 | H (B) | 5S rRNA | polymer | 120 | 38814.1 | 1 | GenBank (1700933240) | Escherichia coli | |
| 9 | I (D) | Large ribosomal subunit protein uL2 | polymer | 273 | 29923.6 | 1 | UniProt (P60422) Pfam (PF00181) Pfam (PF03947) | Escherichia coli | 50S ribosomal protein L2 |
| 10 | J (E) | 50S ribosomal protein L3 | polymer | 209 | 22291.6 | 1 | UniProt (P60438) Pfam (PF00297) | Escherichia coli | Large ribosomal subunit protein uL3 |
| 11 | K (F) | 50S ribosomal protein L4 | polymer | 201 | 22121.6 | 1 | UniProt (P60723) Pfam (PF00573) | Escherichia coli | Large ribosomal subunit protein uL4 |
| 12 | L (G) | Large ribosomal subunit protein uL5 | polymer | 179 | 20333.6 | 1 | UniProt (P62399) Pfam (PF00281) Pfam (PF00673) | Escherichia coli | 50S ribosomal protein L5 |
| 13 | M (H) | Large ribosomal subunit protein uL6 | polymer | 177 | 18932.8 | 1 | UniProt (P0AG55) Pfam (PF00347) | Escherichia coli | 50S ribosomal protein L6 |
| 14 | N (I) | Large ribosomal subunit protein bL9 | polymer | 41 | 4330.1 | 1 | UniProt (P0A7R1) Pfam (PF01281) | Escherichia coli | 50S ribosomal protein L9 |
| 15 | O (L) | 50S ribosomal protein L13 | polymer | 142 | 16050.6 | 1 | UniProt (P0AA10) Pfam (PF00572) | Escherichia coli | Large ribosomal subunit protein uL13 |
| 16 | P (M) | 50S ribosomal protein L14 | polymer | 123 | 13565.1 | 1 | UniProt (P0ADY3) Pfam (PF00238) | Escherichia coli | Large ribosomal subunit protein uL14 |
| 17 | Q (N) | Large ribosomal subunit protein uL15 | polymer | 144 | 14994.4 | 1 | UniProt (A7ZSJ0) Pfam (PF00828) | Escherichia coli | 50S ribosomal protein L15 |
| 18 | R (O) | Large ribosomal subunit protein uL16 | polymer | 136 | 15327.3 | 1 | UniProt (P0ADY7) Pfam (PF00252) | Escherichia coli | 50S ribosomal protein L16 |
| 19 | S (P) | Large ribosomal subunit protein bL17 | polymer | 127 | 14393.7 | 1 | UniProt (P0AG44) Pfam (PF01196) | Escherichia coli | 50S ribosomal protein L17 |
| 20 | T (Q) | Large ribosomal subunit protein uL18 | polymer | 117 | 12794.7 | 1 | UniProt (P0C018) Pfam (PF00861) | Escherichia coli | 50S ribosomal protein L18 |
| 21 | U (R) | Large ribosomal subunit protein bL19 | polymer | 115 | 13159.3 | 1 | UniProt (P0A7K6) Pfam (PF01245) | Escherichia coli | 50S ribosomal protein L19 |
| 22 | V (S) | Large ribosomal subunit protein bL20 | polymer | 118 | 13528.0 | 1 | UniProt (P0A7L3) Pfam (PF00453) | Escherichia coli | 50S ribosomal protein L20 |
| 23 | W (T) | 50S ribosomal protein L21 | polymer | 103 | 11586.4 | 1 | UniProt (P0AG48) Pfam (PF00829) | Escherichia coli | Large ribosomal subunit protein bL21 |
| 24 | X (U) | 50S ribosomal protein L22 | polymer | 110 | 12253.4 | 1 | UniProt (P61175) Pfam (PF00237) | Escherichia coli | Large ribosomal subunit protein uL22 |
| 25 | Y (V) | Large ribosomal subunit protein uL23 | polymer | 100 | 11222.2 | 1 | UniProt (P0ADZ0) Pfam (PF00276) | Escherichia coli | 50S ribosomal protein L23 |
| 26 | Z (W) | Large ribosomal subunit protein uL24 | polymer | 103 | 11210.1 | 1 | UniProt (P60624) Pfam (PF00467) Pfam (PF17136) | Escherichia coli | 50S ribosomal protein L24 |
| 27 | AA (X) | 50S ribosomal protein L25 | polymer | 94 | 10713.5 | 1 | UniProt (P68919) Pfam (PF01386) | Escherichia coli | Large ribosomal subunit protein bL25 |
| 28 | BA (Y) | Large ribosomal subunit protein bL27 | polymer | 85 | 9146.5 | 1 | UniProt (P0A7L8) Pfam (PF01016) | Escherichia coli | 50S ribosomal protein L27 |
| 29 | CA (Z) | Large ribosomal subunit protein bL28 | polymer | 78 | 9027.6 | 1 | UniProt (P0A7M2) Pfam (PF00830) | Escherichia coli | 50S ribosomal protein L28 |
| 30 | DA (2) | Large ribosomal subunit protein bL31 | polymer | 67 | 7613.8 | 1 | UniProt (P0A7M9) Pfam (PF01197) | Escherichia coli | 50S ribosomal protein L31 |
| 31 | EA (A) | 23S rRNA | polymer | 2904 | 941811.6 | 1 | Escherichia coli | ||
| 32 | FA (a) | 16S rRNA | polymer | 1542 | 499873.4 | 1 | GenBank (1758835854) | Escherichia coli | |
| 33 | GA (b) | Small ribosomal subunit protein uS2 | polymer | 241 | 26795.7 | 1 | UniProt (A7ZHQ9) Pfam (PF00318) | Escherichia coli | 30S ribosomal protein S2 |
| 34 | HA (c) | Small ribosomal subunit protein uS3 | polymer | 233 | 26031.3 | 1 | UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189) | Escherichia coli | 30S ribosomal protein S3 |
| 35 | IA (d) | Small ribosomal subunit protein uS4 | polymer | 206 | 23514.2 | 1 | UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479) | Escherichia coli | 30S ribosomal protein S4 |
| 36 | JA (e) | Small ribosomal subunit protein uS5 | polymer | 167 | 17629.4 | 1 | UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719) | Escherichia coli | 30S ribosomal protein S5 |
| 37 | KA (f) | Small ribosomal subunit protein bS6, fully modified isoform | polymer | 102 | 11897.7 | 1 | UniProt (P02358) Pfam (PF01250) | Escherichia coli | |
| 38 | LA (g) | Small ribosomal subunit protein uS7 | polymer | 179 | 20055.2 | 1 | UniProt (P02359) Pfam (PF00177) | Escherichia coli | 30S ribosomal protein S7 |
| 39 | MA (h) | Small ribosomal subunit protein uS8 | polymer | 130 | 14146.6 | 1 | UniProt (P0A7W7) Pfam (PF00410) | Escherichia coli | 30S ribosomal protein S8 |
| 40 | NA (i) | Small ribosomal subunit protein uS9 | polymer | 130 | 14886.3 | 1 | UniProt (P0A7X3) Pfam (PF00380) | Escherichia coli | 30S ribosomal protein S9 |
| 41 | OA (j) | Small ribosomal subunit protein uS10 | polymer | 103 | 11755.6 | 1 | UniProt (P0A7R5) Pfam (PF00338) | Escherichia coli | 30S ribosomal protein S10,Transcription termination/antitermination protein NusE |
| 42 | PA (k) | Small ribosomal subunit protein uS11 | polymer | 129 | 13872.0 | 1 | UniProt (P0A7R9) Pfam (PF00411) | Escherichia coli | 30S ribosomal protein S11 |
| 43 | QA (l) | Small ribosomal subunit protein uS12 | polymer | 124 | 13814.2 | 1 | UniProt (P0A7S3) Pfam (PF00164) | Escherichia coli | 30S ribosomal protein S12 |
| 44 | RA (m) | Small ribosomal subunit protein uS13 | polymer | 118 | 13128.5 | 1 | UniProt (P0A7S9) Pfam (PF00416) | Escherichia coli | 30S ribosomal protein S13 |
| 45 | SA (n) | Small ribosomal subunit protein uS14 | polymer | 101 | 11606.6 | 1 | UniProt (P0AG59) Pfam (PF00253) | Escherichia coli | 30S ribosomal protein S14 |
| 46 | TA (o) | Small ribosomal subunit protein uS15 | polymer | 89 | 10290.8 | 1 | UniProt (P0ADZ4) Pfam (PF00312) | Escherichia coli | 30S ribosomal protein S15 |
| 47 | UA (p) | Small ribosomal subunit protein bS16 | polymer | 82 | 9207.6 | 1 | UniProt (P0A7T3) Pfam (PF00886) | Escherichia coli | 30S ribosomal protein S16 |
| 48 | VA (q) | Small ribosomal subunit protein uS17 | polymer | 84 | 9724.5 | 1 | UniProt (P0AG63) Pfam (PF00366) | Escherichia coli | 30S ribosomal protein S17 |
| 49 | WA (r) | Small ribosomal subunit protein bS18 | polymer | 75 | 9005.5 | 1 | UniProt (P0A7T7) Pfam (PF01084) | Escherichia coli | 30S ribosomal protein S18 |
| 50 | XA (s) | Small ribosomal subunit protein uS19 | polymer | 92 | 10455.4 | 1 | UniProt (P0A7U3) Pfam (PF00203) | Escherichia coli | 30S ribosomal protein S19 |
| 51 | YA (t) | Small ribosomal subunit protein bS20 | polymer | 87 | 9708.5 | 1 | UniProt (P0A7U7) Pfam (PF01649) | Escherichia coli | 30S ribosomal protein S20 |
| 52 | ZA (u) | 30S ribosomal protein S21 | polymer | 71 | 8524.0 | 1 | UniProt (P68679) Pfam (PF01165) | Escherichia coli | Small ribosomal subunit protein bS21 |
| 53 | AB (v) | Ribosome hibernation promoting factor | polymer | 95 | 10767.2 | 1 | UniProt (P0AFX0) Pfam (PF02482) | Escherichia coli | HPF,Hibernation factor HPF |
| 54 | BB (y) | Ribosome modulation factor | polymer | 55 | 6520.5 | 1 | UniProt (P0AFW2) Pfam (PF04957) | Escherichia coli | RMF,Hibernation factor RMF,Protein E |
| 55 | CB (z) | Ribonuclease I | polymer | 268 | 29673.7 | 1 | UniProt (P21338) Pfam (PF00445) | Escherichia coli | RNase I,Enterobacter ribonuclease |
| 56 | DB (8) | Small ribosomal subunit protein bS1 | polymer | 557 | 61238.9 | 1 | UniProt (P0AG67) Pfam (PF00575) | Escherichia coli | 30S ribosomal protein S1,Bacteriophage Q beta RNA-directed RNA polymerase subunit I |
| 57 | AC, AD, AE, AF, AG... (A, a, 3, B, D...) | MAGNESIUM ION | non-polymer | 24.3 | 475 | Chemie (MG) | |||
| 58 | LT (z) | CALCIUM ION | non-polymer | 40.1 | 1 | Chemie (CA) | |||
| 59 | MT, NT, OT, PT (N, Y, A, a) | water | water | 18.0 | 32 | Chemie (HOH) |
Sequence modifications
k: 1 - 129 (UniProt: P0A7R9)
z: -22 - 245 (UniProt: P21338)
| PDB | External Database | Details |
|---|---|---|
| Ias 119 | Asn 119 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Phe 55 | His 78 | engineered mutation |
| Phe 133 | His 156 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 56 |
| Total formula weight | 2233049.5 | |
| Non-Polymers* | Number of molecules | 476 |
| Total formula weight | 11585.0 | |
| All* | Total formula weight | 2244634.5 |
