6WD9
Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure III-B)
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 | b | 50S ribosomal protein L2 | polymer | 271 | 29663.2 | 1 | UniProt (P60422) Pfam (PF00181) Pfam (PF03947) In PDB | Escherichia coli | Large ribosomal subunit protein uL2 |
2 | c | 50S ribosomal protein L3 | polymer | 209 | 22277.5 | 1 | UniProt (P60438) Pfam (PF00297) In PDB | Escherichia coli | Large ribosomal subunit protein uL3 |
3 | d | 50S ribosomal protein L4 | polymer | 201 | 22121.6 | 1 | UniProt (D7Z9F6) Pfam (PF00573) UniProt (by SIFTS) (P60723) In PDB | Escherichia coli | |
4 | e | 50S ribosomal protein L5 | polymer | 177 | 20073.2 | 1 | UniProt (S1EUW9) Pfam (PF00281) Pfam (PF00673) UniProt (by SIFTS) (P62399) In PDB | Escherichia coli | |
5 | f | 50S ribosomal protein L6 | polymer | 176 | 18801.6 | 1 | UniProt (E9YV47) Pfam (PF00347) UniProt (by SIFTS) (P0AG55) In PDB | Escherichia coli | |
6 | g | 50S ribosomal protein L9 | polymer | 149 | 15789.0 | 1 | UniProt (D7ZI15) Pfam (PF01281) Pfam (PF03948) UniProt (by SIFTS) (P0A7R1) In PDB | Escherichia coli | |
7 | h | 50S ribosomal protein L10 | polymer | 131 | 14112.3 | 1 | UniProt (D6I3M6) Pfam (PF00466) UniProt (by SIFTS) (P0A7J3) In PDB | Escherichia coli | |
8 | i | 50S ribosomal protein L11 | polymer | 141 | 14763.2 | 1 | UniProt (S1ERR4) Pfam (PF03946) Pfam (PF00298) UniProt (by SIFTS) (P0A7J7) In PDB | Escherichia coli | |
9 | j | 50S ribosomal protein L13 | polymer | 142 | 16050.6 | 1 | UniProt (D7ZET0) Pfam (PF00572) UniProt (by SIFTS) (P0AA10) In PDB | Escherichia coli | |
10 | k | 50S ribosomal protein L14 | polymer | 122 | 13451.9 | 1 | UniProt (U9YFU2) Pfam (PF00238) UniProt (by SIFTS) (P0ADY3) In PDB | Escherichia coli | |
11 | l | 50S ribosomal protein L15 | polymer | 143 | 14877.3 | 1 | UniProt (A0A037Y8L6) Pfam (PF00828) UniProt (by SIFTS) (P02413) In PDB | Escherichia coli | |
12 | m | 50S ribosomal protein L16 | polymer | 136 | 15312.3 | 1 | UniProt (P0ADY7) Pfam (PF00252) In PDB | Escherichia coli | Large ribosomal subunit protein uL16 |
13 | n | 50S ribosomal protein L17 | polymer | 120 | 13721.9 | 1 | UniProt (D6I1Y5) Pfam (PF01196) UniProt (by SIFTS) (P0AG44) In PDB | Escherichia coli | |
14 | o | 50S ribosomal protein L18 | polymer | 116 | 12663.5 | 1 | UniProt (F4TL27) Pfam (PF00861) UniProt (by SIFTS) (P0C018) In PDB | Escherichia coli | |
15 | p | 50S ribosomal protein L19 | polymer | 114 | 13028.1 | 1 | UniProt (I2XAW2) Pfam (PF01245) UniProt (by SIFTS) (P0A7K6) In PDB | Escherichia coli | |
16 | q | 50S ribosomal protein L20 | polymer | 117 | 13396.8 | 1 | UniProt (L3CCT0) Pfam (PF00453) UniProt (by SIFTS) (P0A7L3) In PDB | Escherichia coli | |
17 | r | 50S ribosomal protein L21 | polymer | 103 | 11586.4 | 1 | UniProt (D7ZEN7) Pfam (PF00829) UniProt (by SIFTS) (P0AG48) In PDB | Escherichia coli | |
18 | s | 50S ribosomal protein L22 | polymer | 110 | 12253.4 | 1 | UniProt (D7Z9G0) Pfam (PF00237) UniProt (by SIFTS) (P61175) In PDB | Escherichia coli | |
19 | t | 50S ribosomal protein L23 | polymer | 93 | 10546.5 | 1 | UniProt (D6I208) Pfam (PF00276) UniProt (by SIFTS) (P0ADZ0) In PDB | Escherichia coli | |
20 | u | 50S ribosomal protein L24 | polymer | 102 | 11078.9 | 1 | UniProt (D7XKZ6) Pfam (PF00467) Pfam (PF17136) UniProt (by SIFTS) (P60624) In PDB | Escherichia coli | |
21 | v | 50S ribosomal protein L25 | polymer | 94 | 10713.5 | 1 | UniProt (D7XH79) Pfam (PF01386) UniProt (by SIFTS) (P68919) In PDB | Escherichia coli | |
22 | w | 50S ribosomal protein L27 | polymer | 75 | 8174.4 | 1 | UniProt (I2X5R7) Pfam (PF01016) UniProt (by SIFTS) (P0A7L8) In PDB | Escherichia coli | |
23 | x | 50S ribosomal protein L28 | polymer | 77 | 8896.4 | 1 | UniProt (J7RMJ2) Pfam (PF00830) UniProt (by SIFTS) (P0A7M2) In PDB | Escherichia coli | |
24 | y | 50S ribosomal protein L29 | polymer | 63 | 7286.5 | 1 | UniProt (D7Z9G3) Pfam (PF00831) UniProt (by SIFTS) (P0A7M6) In PDB | Escherichia coli | |
25 | z | 50S ribosomal protein L30 | polymer | 58 | 6423.6 | 1 | UniProt (I2X1N4) Pfam (PF00327) UniProt (by SIFTS) (P0AG51) In PDB | Escherichia coli | |
26 | B | 50S ribosomal protein L32 | polymer | 56 | 6332.2 | 1 | UniProt (E3PJQ3) Pfam (PF01783) UniProt (by SIFTS) (P0A7N4) In PDB | Escherichia coli | |
27 | C | 50S ribosomal protein L33 | polymer | 50 | 5814.8 | 1 | UniProt (L3NSS9) Pfam (PF00471) UniProt (by SIFTS) (P0A7N9) In PDB | Escherichia coli | |
28 | D | 50S ribosomal protein L34 | polymer | 46 | 5397.5 | 1 | UniProt (B7MGC4) Pfam (PF00468) UniProt (by SIFTS) (P0A7P5) In PDB | Escherichia coli | |
29 | E | 50S ribosomal protein L35 | polymer | 64 | 7181.8 | 1 | UniProt (G0F552) Pfam (PF01632) UniProt (by SIFTS) (P0A7Q1) In PDB | Escherichia coli | |
30 | F | 50S ribosomal protein L36 | polymer | 38 | 4377.4 | 1 | UniProt (A0A0E2L017) Pfam (PF00444) UniProt (by SIFTS) (P0A7Q6) In PDB | Escherichia coli | |
31 | G | 30S ribosomal protein S2 | polymer | 225 | 25015.8 | 1 | UniProt (C3TPN2) Pfam (PF00318) UniProt (by SIFTS) (P0A7V0) In PDB | Escherichia coli | |
32 | H | 30S ribosomal protein S3 | polymer | 206 | 23078.8 | 1 | UniProt (A0A376HTV6) Pfam (PF07650) Pfam (PF00189) UniProt (by SIFTS) (P0A7V3) In PDB | Escherichia coli | |
33 | I | 30S ribosomal protein S4 | polymer | 205 | 23383.0 | 1 | UniProt (L3PZ69) Pfam (PF00163) Pfam (PF01479) UniProt (by SIFTS) (P0A7V8) In PDB | Escherichia coli | |
34 | J | 30S ribosomal protein S5 | polymer | 157 | 16532.1 | 1 | UniProt (F4TL26) Pfam (PF00333) Pfam (PF03719) UniProt (by SIFTS) (P0A7W1) In PDB | Escherichia coli | |
35 | K | 30S ribosomal protein S6 | polymer | 100 | 11669.4 | 1 | UniProt (S1CG62) Pfam (PF01250) UniProt (by SIFTS) (P02358) In PDB | Escherichia coli | |
36 | L | 30S ribosomal protein S7 | polymer | 151 | 16861.5 | 1 | UniProt (S1D5F0) Pfam (PF00177) UniProt (by SIFTS) (P02359) In PDB | Escherichia coli | |
37 | M | 30S ribosomal protein S8 | polymer | 129 | 14015.4 | 1 | UniProt (D8A1L7) Pfam (PF00410) UniProt (by SIFTS) (P0A7W7) In PDB | Escherichia coli | |
38 | N | 30S ribosomal protein S9 | polymer | 127 | 14554.9 | 1 | UniProt (T9TH92) Pfam (PF00380) UniProt (by SIFTS) (P0A7X3) In PDB | Escherichia coli | |
39 | O | 30S ribosomal protein S10 | polymer | 98 | 11197.0 | 1 | UniProt (D7X302) Pfam (PF00338) UniProt (by SIFTS) (P0A7R5) In PDB | Escherichia coli | |
40 | P | 30S ribosomal protein S11 | polymer | 116 | 12388.1 | 1 | UniProt (I2UH22) Pfam (PF00411) UniProt (by SIFTS) (P0A7R9) In PDB | Escherichia coli | |
41 | Q | 30S ribosomal protein S12 | polymer | 123 | 13637.0 | 1 | UniProt (V6FZ95) Pfam (PF00164) UniProt (by SIFTS) (P0A7S3) In PDB | Escherichia coli | |
42 | R | 30S ribosomal protein S13 | polymer | 114 | 12625.8 | 1 | UniProt (A0A1X3KX08) Pfam (PF00416) UniProt (by SIFTS) (P0A7S9) In PDB | Escherichia coli | |
43 | S | 30S ribosomal protein S14 | polymer | 100 | 11475.4 | 1 | UniProt (I2X0X3) Pfam (PF00253) UniProt (by SIFTS) (P0AG59) In PDB | Escherichia coli | |
44 | T | 30S ribosomal protein S15 | polymer | 88 | 10159.6 | 1 | UniProt (D7XN21) Pfam (PF00312) UniProt (by SIFTS) (P0ADZ4) In PDB | Escherichia coli | |
45 | U | 30S ribosomal protein S16 | polymer | 82 | 9207.6 | 1 | UniProt (B7MIU7) Pfam (PF00886) UniProt (by SIFTS) (P0A7T3) In PDB | Escherichia coli | |
46 | V | 30S ribosomal protein S17 | polymer | 80 | 9263.9 | 1 | UniProt (A0A080IK26) Pfam (PF00366) UniProt (by SIFTS) (P0AG63) In PDB | Escherichia coli | |
47 | W | 30S ribosomal protein S18 | polymer | 65 | 7606.8 | 1 | UniProt (E0J6I2) Pfam (PF01084) UniProt (by SIFTS) (P0A7T7) In PDB | Escherichia coli | |
48 | X | 30S ribosomal protein S19 | polymer | 79 | 9057.6 | 1 | UniProt (F4SQ43) Pfam (PF00203) UniProt (by SIFTS) (P0A7U3) In PDB | Escherichia coli | |
49 | Y | 30S ribosomal protein S20 | polymer | 85 | 9506.2 | 1 | UniProt (T6N332) Pfam (PF01649) UniProt (by SIFTS) (P0A7U7) In PDB | Escherichia coli | |
50 | Z | 30S ribosomal protein S21 | polymer | 65 | 7763.1 | 1 | UniProt (E9TH65) Pfam (PF01165) UniProt (by SIFTS) (P68679) In PDB | Escherichia coli | |
51 | a | 50S ribosomal protein L1 | polymer | 223 | 23735.5 | 1 | UniProt (A0A4Y8DMK0) Pfam (PF00687) UniProt (by SIFTS) (P0A7L0) In PDB | Escherichia coli | |
52 | 3 | 16S ribosomal RNA | polymer | 1539 | 498725.4 | 1 | GenBank (1338015391) | Escherichia coli | |
53 | 1 | 23S ribosomal RNA | polymer | 2903 | 941305.3 | 1 | GenBank (1036415628) | Escherichia coli | |
54 | 2 | 5S ribosomal RNA | polymer | 120 | 38813.1 | 1 | GenBank (1370526515) | Escherichia coli | |
55 | 5, 6 | tRNAfMet | polymer | 77 | 24802.8 | 2 | GenBank (1384458579) | Escherichia coli | |
56 | 4 | mRNA | polymer | 18 | 5844.6 | 1 | Escherichia coli | ||
57 | 7 | tRNAPhe | polymer | 76 | 24485.5 | 1 | GenBank (1315725308) | Escherichia coli | |
58 | 8 | Elongation factor Tu | polymer | 400 | 44125.2 | 1 | UniProt (E2QFJ4) Pfam (PF00009) Pfam (PF03144) Pfam (PF03143) UniProt (by SIFTS) (P0CE47) In PDB | Escherichia coli | EF-Tu |
59 | 5 | N-FORMYLMETHIONINE | non-polymer | 177.2 | 1 | Chemie (FME) | |||
60 | 7 | PHENYLALANINE | non-polymer | 165.2 | 1 | Chemie (PHE) | |||
61 | 8 | GUANOSINE-5'-DIPHOSPHATE | non-polymer | 443.2 | 1 | Chemie (GDP) |
Sequence modifications
1: 1 - 2903 (GenBank: 1036415628)
2: 1 - 119 (GenBank: 1370526515)
8: 2 - 394 (UniProt: E2QFJ4)
PDB | External Database | Details |
---|---|---|
C 747 | U 1155325 | conflict |
PDB | External Database | Details |
---|---|---|
A 120 | - | insertion |
PDB | External Database | Details |
---|---|---|
Ser 395 | - | expression tag |
His 396 | - | expression tag |
His 397 | - | expression tag |
His 398 | - | expression tag |
His 399 | - | expression tag |
His 400 | - | expression tag |
His 401 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 59 |
Total formula weight | 2281806.2 | |
Non-Polymers* | Number of molecules | 3 |
Total formula weight | 785.6 | |
All* | Total formula weight | 2282591.8 |