6TBV
Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 2)
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 (16S1) | 16S rRNA | polymer | 1534 | 497405.0 | 1 | GenBank (1108560344) | Escherichia coli K-12 | |
| 2 | B (S021) | 30S ribosomal protein S2 | polymer | 241 | 26781.7 | 1 | UniProt (P0A7V0) Pfam (PF00318) | Escherichia coli K-12 | Small ribosomal subunit protein uS2 |
| 3 | C (S031) | 30S ribosomal protein S3 | polymer | 233 | 26031.3 | 1 | UniProt (P0A7V3) Pfam (PF07650) Pfam (PF00189) | Escherichia coli K-12 | Small ribosomal subunit protein uS3 |
| 4 | D (S041) | 30S ribosomal protein S4 | polymer | 206 | 23514.2 | 1 | UniProt (P0A7V8) Pfam (PF00163) Pfam (PF01479) | Escherichia coli K-12 | Small ribosomal subunit protein uS4 |
| 5 | E (S051) | 30S ribosomal protein S5 | polymer | 167 | 17629.4 | 1 | UniProt (P0A7W1) Pfam (PF00333) Pfam (PF03719) | Escherichia coli K-12 | Small ribosomal subunit protein uS5 |
| 6 | F (S061) | 30S ribosomal protein S6 | polymer | 135 | 15727.5 | 1 | UniProt (P02358) Pfam (PF01250) | Escherichia coli K-12 | Small ribosomal subunit protein bS6 |
| 7 | G (S071) | 30S ribosomal protein S7 | polymer | 179 | 20055.2 | 1 | UniProt (P02359) Pfam (PF00177) | Escherichia coli K-12 | Small ribosomal subunit protein uS7 |
| 8 | H (S081) | 30S ribosomal protein S8 | polymer | 130 | 14146.6 | 1 | UniProt (P0A7W7) Pfam (PF00410) | Escherichia coli K-12 | Small ribosomal subunit protein uS8 |
| 9 | I (S091) | 30S ribosomal protein S9 | polymer | 130 | 14886.3 | 1 | UniProt (P0A7X3) Pfam (PF00380) | Escherichia coli K-12 | Small ribosomal subunit protein uS9 |
| 10 | J (S101) | 30S ribosomal protein S10 | polymer | 103 | 11755.6 | 1 | UniProt (P0A7R5) Pfam (PF00338) | Escherichia coli K-12 | Small ribosomal subunit protein uS10 |
| 11 | K (S111) | 30S ribosomal protein S11 | polymer | 129 | 13871.0 | 1 | UniProt (P0A7R9) Pfam (PF00411) | Escherichia coli K-12 | Small ribosomal subunit protein uS11 |
| 12 | L (S121) | 30S ribosomal protein S12 | polymer | 124 | 13814.2 | 1 | UniProt (P0A7S3) Pfam (PF00164) | Escherichia coli K-12 | Small ribosomal subunit protein uS12 |
| 13 | M (S131) | 30S ribosomal protein S13 | polymer | 118 | 13128.5 | 1 | UniProt (P0A7S9) Pfam (PF00416) | Escherichia coli K-12 | Small ribosomal subunit protein uS13 |
| 14 | N (S141) | 30S ribosomal protein S14 | polymer | 102 | 11677.6 | 1 | UniProt (P0AG59) Pfam (PF00253) | Escherichia coli K-12 | Small ribosomal subunit protein uS14 |
| 15 | O (S151) | 30S ribosomal protein S15 | polymer | 89 | 10290.8 | 1 | UniProt (P0ADZ4) Pfam (PF00312) | Escherichia coli K-12 | Small ribosomal subunit protein uS15 |
| 16 | P (S161) | 30S ribosomal protein S16 | polymer | 82 | 9207.6 | 1 | UniProt (P0A7T3) Pfam (PF00886) | Escherichia coli K-12 | Small ribosomal subunit protein bS16 |
| 17 | Q (S171) | 30S ribosomal protein S17 | polymer | 84 | 9724.5 | 1 | UniProt (P0AG63) Pfam (PF00366) | Escherichia coli K-12 | Small ribosomal subunit protein uS17 |
| 18 | R (S181) | 30S ribosomal protein S18 | polymer | 75 | 9005.5 | 1 | UniProt (P0A7T7) Pfam (PF01084) | Escherichia coli K-12 | Small ribosomal subunit protein bS18 |
| 19 | S (S191) | 30S ribosomal protein S19 | polymer | 92 | 10455.4 | 1 | UniProt (P0A7U3) Pfam (PF00203) | Escherichia coli K-12 | Small ribosomal subunit protein uS19 |
| 20 | T (S201) | 30S ribosomal protein S20 | polymer | 87 | 9708.5 | 1 | UniProt (P0A7U7) Pfam (PF01649) | Escherichia coli K-12 | Small ribosomal subunit protein bS20 |
| 21 | U (S211) | 30S ribosomal protein S21 | polymer | 71 | 8524.0 | 1 | UniProt (P68679) Pfam (PF01165) | Escherichia coli K-12 | Small ribosomal subunit protein bS21 |
| 22 | V (23S1) | 23S rRNA | polymer | 2897 | 939607.3 | 1 | Escherichia coli K-12 | ||
| 23 | W (05S1) | 5S rRNA | polymer | 120 | 38790.1 | 1 | GenBank (1726050194) | Escherichia coli K-12 | |
| 24 | X (L021) | 50S ribosomal protein L2 | polymer | 273 | 29923.6 | 1 | UniProt (P60422) Pfam (PF00181) Pfam (PF03947) | Escherichia coli K-12 | Large ribosomal subunit protein uL2 |
| 25 | Y (L031) | 50S ribosomal protein L3 | polymer | 209 | 22291.6 | 1 | UniProt (P60438) Pfam (PF00297) | Escherichia coli K-12 | Large ribosomal subunit protein uL3 |
| 26 | Z (L041) | 50S ribosomal protein L4 | polymer | 201 | 22121.6 | 1 | UniProt (P60723) Pfam (PF00573) | Escherichia coli K-12 | Large ribosomal subunit protein uL4 |
| 27 | AA (L051) | 50S ribosomal protein L5 | polymer | 179 | 20333.6 | 1 | UniProt (P62399) Pfam (PF00281) Pfam (PF00673) | Escherichia coli K-12 | Large ribosomal subunit protein uL5 |
| 28 | BA (L061) | 50S ribosomal protein L6 | polymer | 177 | 18932.8 | 1 | UniProt (P0AG55) Pfam (PF00347) | Escherichia coli K-12 | Large ribosomal subunit protein uL6 |
| 29 | CA (L091) | 50S ribosomal protein L9 | polymer | 149 | 15789.0 | 1 | UniProt (P0A7R1) Pfam (PF03948) Pfam (PF01281) | Escherichia coli K-12 | Large ribosomal subunit protein bL9 |
| 30 | DA (L311) | 50S ribosomal protein L31 | polymer | 70 | 7887.1 | 1 | UniProt (P0A7M9) Pfam (PF01197) | Escherichia coli K-12 | Large ribosomal subunit protein bL31-A |
| 31 | EA (L131) | 50S ribosomal protein L13 | polymer | 142 | 16050.6 | 1 | UniProt (P0AA10) Pfam (PF00572) | Escherichia coli K-12 | Large ribosomal subunit protein uL13 |
| 32 | FA (L141) | 50S ribosomal protein L14 | polymer | 123 | 13565.1 | 1 | UniProt (P0ADY3) Pfam (PF00238) | Escherichia coli K-12 | Large ribosomal subunit protein uL14 |
| 33 | GA (L151) | 50S ribosomal protein L15 | polymer | 144 | 15008.5 | 1 | UniProt (P02413) Pfam (PF00828) | Escherichia coli K-12 | Large ribosomal subunit protein uL15 |
| 34 | HA (L161) | 50S ribosomal protein L16 | polymer | 136 | 15327.3 | 1 | UniProt (P0ADY7) Pfam (PF00252) | Escherichia coli K-12 | Large ribosomal subunit protein uL16 |
| 35 | IA (L171) | 50S ribosomal protein L17 | polymer | 127 | 14393.7 | 1 | UniProt (P0AG44) Pfam (PF01196) | Escherichia coli K-12 | Large ribosomal subunit protein bL17 |
| 36 | JA (L181) | 50S ribosomal protein L18 | polymer | 117 | 12794.7 | 1 | UniProt (P0C018) Pfam (PF00861) | Escherichia coli K-12 | Large ribosomal subunit protein uL18 |
| 37 | KA (L191) | 50S ribosomal protein L19 | polymer | 115 | 13159.3 | 1 | UniProt (P0A7K6) Pfam (PF01245) | Escherichia coli K-12 | Large ribosomal subunit protein bL19 |
| 38 | LA (L201) | 50S ribosomal protein L20 | polymer | 118 | 13528.0 | 1 | UniProt (P0A7L3) Pfam (PF00453) | Escherichia coli K-12 | Large ribosomal subunit protein bL20 |
| 39 | MA (L211) | 50S ribosomal protein L21 | polymer | 103 | 11586.4 | 1 | UniProt (P0AG48) Pfam (PF00829) | Escherichia coli K-12 | Large ribosomal subunit protein bL21 |
| 40 | NA (L221) | 50S ribosomal protein L22 | polymer | 110 | 12253.4 | 1 | UniProt (P61175) Pfam (PF00237) | Escherichia coli K-12 | Large ribosomal subunit protein uL22 |
| 41 | OA (L231) | 50S ribosomal protein L23 | polymer | 100 | 11222.2 | 1 | UniProt (P0ADZ0) Pfam (PF00276) | Escherichia coli K-12 | Large ribosomal subunit protein uL23 |
| 42 | PA (L241) | 50S ribosomal protein L24 | polymer | 104 | 11339.3 | 1 | UniProt (P60624) Pfam (PF00467) Pfam (PF17136) | Escherichia coli K-12 | Large ribosomal subunit protein uL24 |
| 43 | QA (L251) | 50S ribosomal protein L25 | polymer | 94 | 10713.5 | 1 | UniProt (P68919) Pfam (PF01386) | Escherichia coli K-12 | Large ribosomal subunit protein bL25 |
| 44 | RA (L271) | 50S ribosomal protein L27 | polymer | 85 | 9146.5 | 1 | UniProt (P0A7L8) Pfam (PF01016) | Escherichia coli K-12 | Large ribosomal subunit protein bL27 |
| 45 | SA (L281) | 50S ribosomal protein L28 | polymer | 78 | 9027.6 | 1 | UniProt (P0A7M2) Pfam (PF00830) | Escherichia coli K-12 | Large ribosomal subunit protein bL28 |
| 46 | TA (L291) | 50S ribosomal protein L29 | polymer | 63 | 7286.5 | 1 | UniProt (P0A7M6) Pfam (PF00831) | Escherichia coli K-12 | Large ribosomal subunit protein uL29 |
| 47 | UA (L301) | 50S ribosomal protein L30 | polymer | 59 | 6554.8 | 1 | UniProt (P0AG51) Pfam (PF00327) | Escherichia coli K-12 | Large ribosomal subunit protein uL30 |
| 48 | VA (L321) | 50S ribosomal protein L32 | polymer | 57 | 6463.4 | 1 | UniProt (P0A7N4) Pfam (PF01783) | Escherichia coli K-12 | Large ribosomal subunit protein bL32 |
| 49 | WA (L331) | 50S ribosomal protein L33 | polymer | 55 | 6388.6 | 1 | UniProt (P0A7N9) Pfam (PF00471) | Escherichia coli K-12 | Large ribosomal subunit protein bL33 |
| 50 | XA (L341) | 50S ribosomal protein L34 | polymer | 46 | 5397.5 | 1 | UniProt (P0A7P5) Pfam (PF00468) | Escherichia coli K-12 | Large ribosomal subunit protein bL34 |
| 51 | YA (L351) | 50S ribosomal protein L35 | polymer | 65 | 7313.0 | 1 | UniProt (P0A7Q1) Pfam (PF01632) | Escherichia coli K-12 | Large ribosomal subunit protein bL35,Ribosomal protein A |
| 52 | ZA (L361) | 50S ribosomal protein L36 | polymer | 38 | 4377.4 | 1 | UniProt (P0A7Q6) Pfam (PF00444) | Escherichia coli K-12 | Large ribosomal subunit protein bL36-A,Ribosomal protein B |
| 53 | AB (SPE1) | SpeFL | polymer | 34 | 4286.9 | 1 | UniProt (A0A4S4NWS2) UniProt (by SIFTS) (P0DTV7) | Escherichia coli K-12 | |
| 54 | BB (MRN1) | mRNA | polymer | 7 | 2173.3 | 1 | Escherichia coli K-12 | ||
| 55 | CB (PTR1) | P-site Arg-tRNA | polymer | 76 | 24582.8 | 1 | Escherichia coli K-12 | ||
| 56 | AC, AD, AE, AM, AN... (16S1, 23S1, PTR1, L231) | MAGNESIUM ION | non-polymer | 24.3 | 339 | Chemie (MG) | |||
| 57 | AF, AW, AX, AY, AZ... (16S1, 23S1, L031, L161, 05S1) | POTASSIUM ION | non-polymer | 39.1 | 147 | Chemie (K) | |||
| 58 | AAA, AAB, ABA, ABB, ACA... (23S1, 16S1, 05S1, L021, L041...) | UNKNOWN ATOM OR ION | non-polymer | 35.5 | 1201 | Chemie (UNX) | |||
| 59 | CLB, RL, SNB (L311, S021, L361) | ZINC ION | non-polymer | 65.4 | 3 | Chemie (ZN) | |||
| 60 | YL (23S1) | L-ornithine | non-polymer | 132.2 | 1 | Chemie (ORN) | |||
| 61 | EOB, FOB, GOB, HOB, IOB... (16S1, S111, S131, S141, S171...) | water | water | 18.0 | 800 | Chemie (HOH) |
Sequence modifications
S141: 0 - 101 (UniProt: P0AG59)
SPE1: 1 - 34 (UniProt: A0A4S4NWS2)
| PDB | External Database | Details |
|---|---|---|
| Ala 35 | - | insertion |
| PDB | External Database | Details |
|---|---|---|
| Ser 5 | Asn 5 | conflict |
| Thr 7 | Leu 7 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 55 |
| Total formula weight | 2166956.8 | |
| Non-Polymers* | Number of molecules | 1691 |
| Total formula weight | 56894.2 | |
| All* | Total formula weight | 2223851.1 |
