9VVI
Cryo-EM structure of SecM-arrested 70S ribosome with YheS
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 rRNA | polymer | 1542 | 499873.4 | 1 | GenBank (1758835854) | Escherichia coli | |
| 2 | B (B) | 30S ribosomal protein S2 | polymer | 241 | 26781.7 | 1 | UniProt (P0A7V0) | Escherichia coli | Small ribosomal subunit protein uS2 |
| 3 | C (C) | Small ribosomal subunit protein uS3 | polymer | 233 | 26031.3 | 1 | UniProt (P0A7V3) | Escherichia coli | 30S ribosomal protein S3 |
| 4 | D (D) | Small ribosomal subunit protein uS4 | polymer | 206 | 23514.2 | 1 | UniProt (P0A7V8) | Escherichia coli | 30S ribosomal protein S4 |
| 5 | E (E) | Small ribosomal subunit protein uS5 | polymer | 167 | 17629.4 | 1 | UniProt (P0A7W1) | Escherichia coli | 30S ribosomal protein S5 |
| 6 | F (F) | 30S ribosomal protein S6, fully modified isoform | polymer | 135 | 15727.5 | 1 | UniProt (P02358) | Escherichia coli | |
| 7 | G (G) | Small ribosomal subunit protein uS7 | polymer | 179 | 20055.2 | 1 | UniProt (P02359) | Escherichia coli | 30S ribosomal protein S7 |
| 8 | H (H) | Small ribosomal subunit protein uS8 | polymer | 130 | 14146.6 | 1 | UniProt (P0A7W7) | Escherichia coli | 30S ribosomal protein S8 |
| 9 | I (I) | Small ribosomal subunit protein uS9 | polymer | 130 | 14886.3 | 1 | UniProt (P0A7X3) | Escherichia coli | 30S ribosomal protein S9 |
| 10 | J (J) | Small ribosomal subunit protein uS10 | polymer | 103 | 11755.6 | 1 | UniProt (P0A7R5) | Escherichia coli | 30S ribosomal protein S10,Transcription termination/antitermination protein NusE |
| 11 | K (K) | Small ribosomal subunit protein uS11 | polymer | 129 | 13872.0 | 1 | UniProt (P0A7R9) | Escherichia coli | 30S ribosomal protein S11 |
| 12 | L (L) | Small ribosomal subunit protein uS12 | polymer | 124 | 13814.2 | 1 | UniProt (P0A7S3) | Escherichia coli | 30S ribosomal protein S12 |
| 13 | M (M) | Small ribosomal subunit protein uS13 | polymer | 118 | 13128.5 | 1 | UniProt (P0A7S9) | Escherichia coli | 30S ribosomal protein S13 |
| 14 | N (N) | Small ribosomal subunit protein uS14 | polymer | 101 | 11606.6 | 1 | UniProt (P0AG59) | Escherichia coli | 30S ribosomal protein S14 |
| 15 | O (O) | Small ribosomal subunit protein uS15 | polymer | 89 | 10290.8 | 1 | UniProt (P0ADZ4) | Escherichia coli | 30S ribosomal protein S15 |
| 16 | P (P) | Small ribosomal subunit protein bS16 | polymer | 82 | 9207.6 | 1 | UniProt (P0A7T3) | Escherichia coli | 30S ribosomal protein S16 |
| 17 | Q (Q) | Small ribosomal subunit protein uS17 | polymer | 84 | 9724.5 | 1 | UniProt (P0AG63) | Escherichia coli | 30S ribosomal protein S17 |
| 18 | R (R) | Small ribosomal subunit protein bS18 | polymer | 75 | 9005.5 | 1 | UniProt (P0A7T7) | Escherichia coli | 30S ribosomal protein S18 |
| 19 | S (S) | Small ribosomal subunit protein uS19 | polymer | 92 | 10455.4 | 1 | UniProt (P0A7U3) | Escherichia coli | 30S ribosomal protein S19 |
| 20 | T (T) | Small ribosomal subunit protein bS20 | polymer | 87 | 9708.5 | 1 | UniProt (P0A7U7) | Escherichia coli | 30S ribosomal protein S20 |
| 21 | U (U) | 30S ribosomal protein S21 | polymer | 71 | 8524.0 | 1 | UniProt (P68679) | Escherichia coli | Small ribosomal subunit protein bS21 |
| 22 | V (a) | 23S rRNA | polymer | 2904 | 941811.6 | 1 | Escherichia coli | ||
| 23 | W (b) | 5S rRNA | polymer | 119 | 38483.9 | 1 | GenBank (1815787944) | Escherichia coli | |
| 24 | X (7) | Large ribosomal subunit protein uL1 | polymer | 234 | 24765.7 | 1 | UniProt (A7ZUJ7) | Escherichia coli | 50S ribosomal protein L1 |
| 25 | Y (c) | Large ribosomal subunit protein uL2 | polymer | 273 | 29923.6 | 1 | UniProt (P60422) | Escherichia coli | 50S ribosomal protein L2 |
| 26 | Z (d) | 50S ribosomal protein L3 | polymer | 209 | 22291.6 | 1 | UniProt (P60438) | Escherichia coli | Large ribosomal subunit protein uL3 |
| 27 | AA (e) | 50S ribosomal protein L4 | polymer | 201 | 22121.6 | 1 | UniProt (P60723) | Escherichia coli | Large ribosomal subunit protein uL4 |
| 28 | BA (f) | Large ribosomal subunit protein uL5 | polymer | 179 | 20333.6 | 1 | UniProt (P62399) | Escherichia coli | 50S ribosomal protein L5 |
| 29 | CA (g) | Large ribosomal subunit protein uL6 | polymer | 177 | 18932.8 | 1 | UniProt (P0AG55) | Escherichia coli | 50S ribosomal protein L6 |
| 30 | DA (h) | 50S ribosomal protein L9 | polymer | 149 | 15789.0 | 1 | UniProt (P0A7R1) | Escherichia coli | Large ribosomal subunit protein bL9 |
| 31 | EA (i) | 50S ribosomal protein L13 | polymer | 142 | 16050.6 | 1 | UniProt (P0AA10) | Escherichia coli | Large ribosomal subunit protein uL13 |
| 32 | FA (j) | 50S ribosomal protein L14 | polymer | 123 | 13565.1 | 1 | UniProt (P0ADY3) | Escherichia coli | Large ribosomal subunit protein uL14 |
| 33 | GA (k) | 50S ribosomal protein L15 | polymer | 144 | 15008.5 | 1 | UniProt (P02413) | Escherichia coli | Large ribosomal subunit protein uL15 |
| 34 | HA (l) | 50S ribosomal protein L16 | polymer | 136 | 15343.3 | 1 | UniProt (P0ADY7) | Escherichia coli | Large ribosomal subunit protein uL16 |
| 35 | IA (m) | Large ribosomal subunit protein bL17 | polymer | 127 | 14393.7 | 1 | UniProt (P0AG44) | Escherichia coli | 50S ribosomal protein L17 |
| 36 | JA (n) | Large ribosomal subunit protein uL18 | polymer | 117 | 12794.7 | 1 | UniProt (P0C018) | Escherichia coli | 50S ribosomal protein L18 |
| 37 | KA (o) | Large ribosomal subunit protein bL19 | polymer | 115 | 13159.3 | 1 | UniProt (P0A7K6) | Escherichia coli | 50S ribosomal protein L19 |
| 38 | LA (p) | Large ribosomal subunit protein bL20 | polymer | 118 | 13528.0 | 1 | UniProt (P0A7L3) | Escherichia coli | 50S ribosomal protein L20 |
| 39 | MA (q) | 50S ribosomal protein L21 | polymer | 103 | 11586.4 | 1 | UniProt (P0AG48) | Escherichia coli | Large ribosomal subunit protein bL21 |
| 40 | NA (r) | 50S ribosomal protein L22 | polymer | 110 | 12253.4 | 1 | UniProt (P61175) | Escherichia coli | Large ribosomal subunit protein uL22 |
| 41 | OA (s) | Large ribosomal subunit protein uL23 | polymer | 100 | 11222.2 | 1 | UniProt (P0ADZ0) | Escherichia coli | 50S ribosomal protein L23 |
| 42 | PA (t) | 50S ribosomal protein L24 | polymer | 104 | 11339.3 | 1 | UniProt (P60624) | Escherichia coli | Large ribosomal subunit protein uL24 |
| 43 | QA (u) | 50S ribosomal protein L25 | polymer | 94 | 10713.5 | 1 | UniProt (P68919) | Escherichia coli | Large ribosomal subunit protein bL25 |
| 44 | RA (v) | Large ribosomal subunit protein bL27 | polymer | 85 | 9146.5 | 1 | UniProt (P0A7L8) | Escherichia coli | 50S ribosomal protein L27 |
| 45 | SA (w) | Large ribosomal subunit protein bL28 | polymer | 78 | 9027.6 | 1 | UniProt (P0A7M2) | Escherichia coli | 50S ribosomal protein L28 |
| 46 | TA (x) | Large ribosomal subunit protein uL29 | polymer | 63 | 7286.5 | 1 | UniProt (P0A7M6) | Escherichia coli | 50S ribosomal protein L29 |
| 47 | UA (y) | Large ribosomal subunit protein uL30 | polymer | 59 | 6554.8 | 1 | UniProt (P0AG51) | Escherichia coli | 50S ribosomal protein L30 |
| 48 | VA (4) | 50S ribosomal protein L31 | polymer | 70 | 7887.1 | 1 | UniProt (P0A7M9) | Escherichia coli | Large ribosomal subunit protein bL31-A |
| 49 | WA (z) | Large ribosomal subunit protein bL32 | polymer | 57 | 6463.4 | 1 | UniProt (P0A7N4) | Escherichia coli | 50S ribosomal protein L32 |
| 50 | XA (0) | Large ribosomal subunit protein bL33 | polymer | 55 | 6388.6 | 1 | UniProt (P0A7N9) | Escherichia coli | 50S ribosomal protein L33 |
| 51 | YA (1) | 50S ribosomal protein L34 | polymer | 46 | 5397.5 | 1 | UniProt (P0A7P5) | Escherichia coli | Large ribosomal subunit protein bL34 |
| 52 | ZA (2) | Large ribosomal subunit protein bL35 | polymer | 65 | 7313.0 | 1 | UniProt (P0A7Q1) | Escherichia coli | 50S ribosomal protein L35,Ribosomal protein A |
| 53 | AB (3) | 50S ribosomal protein L36 | polymer | 38 | 4377.4 | 1 | UniProt (P0A7Q6) | Escherichia coli | Large ribosomal subunit protein bL36-A,Ribosomal protein B |
| 54 | BB (W) | Probable ATP-binding protein YheS | polymer | 647 | 73119.6 | 1 | UniProt (P63390) | Escherichia coli | |
| 55 | CB (X) | SecM mRNA | polymer | 629 | 201796.6 | 1 | Escherichia coli | ||
| 56 | DB (Y) | A-site tRNA (prolyl-tRNAPro) | polymer | 77 | 24907.8 | 1 | Escherichia coli | ||
| 57 | EB (Z) | P-site tRNA (tRNAGly) | polymer | 76 | 24529.7 | 1 | Escherichia coli | ||
| 58 | FB (6) | Secretion monitor | polymer | 165 | 18305.8 | 1 | UniProt (B7LFW7) | Escherichia coli | |
| 59 | AC, AF, AG, AH, AQ... (A, a, c, e, t...) | POTASSIUM ION | non-polymer | 39.1 | 125 | Chemie (K) PubChem (813) | |||
| 60 | AD, AE, AI, AJ, AK... (A, a, c, d, B...) | MAGNESIUM ION | non-polymer | 24.3 | 269 | Chemie (MG) PubChem (888) | |||
| 61 | MO, NO, OO, PO (a) | SPERMIDINE | non-polymer | 145.2 | 4 | Chemie (SPD) PubChem (1102) | |||
| 62 | JQ, LQ (4, 3) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) PubChem (32051) | |||
| 63 | MQ, NQ (W) | ADENOSINE-5'-TRIPHOSPHATE | non-polymer | 507.2 | 2 | Chemie (ATP) | |||
| 64 | RQ (Y) | PROLINE | non-polymer | 115.1 | 1 | Chemie (PRO) PubChem (145742) | |||
| 65 | TQ (a) | water | water | 18.0 | 18 | Chemie (HOH) |
Sequence modifications
K: 1 - 129 (UniProt: P0A7R9)
l: 1 - 136 (UniProt: P0ADY7)
W: 2 - 637 (UniProt: P63390)
| PDB | External Database | Details |
|---|---|---|
| Ias 119 | Asn 119 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ms6 82 | Met 82 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Met -9 | - | initiating methionine |
| Arg -8 | - | expression tag |
| Gly -7 | - | expression tag |
| His -6 | - | expression tag |
| His -5 | - | expression tag |
| His -4 | - | expression tag |
| His -3 | - | expression tag |
| His -2 | - | expression tag |
| His -1 | - | expression tag |
| Gly 0 | - | expression tag |
| Ser 1 | - | expression tag |
| Gln 175 | Glu 175 | engineered mutation |
| Gln 456 | Glu 456 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 58 |
| Total formula weight | 2507651.5 | |
| Non-Polymers* | Number of molecules | 403 |
| Total formula weight | 13266.6 | |
| All* | Total formula weight | 2520918.1 |
