6N8N

Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit


Sequence Similarity Clusters for the Entities in PDB 6N8N

Entity #1 | Chains: A
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA rna, length: 3396 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #10 | Chains: F
60S ribosomal protein L4-A protein, length: 362 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 259
95 % 54 99 325
90 % 54 99 336
70 % 54 100 375
50 % 71 147 337
40 % 72 183 258
30 % 72 183 276
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 85 301
95 % 54 87 395
90 % 54 87 411
70 % 54 88 444
50 % 71 168 288
40 % 72 170 292
30 % 72 170 316
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 256
95 % 54 95 349
90 % 54 96 357
70 % 54 97 386
50 % 55 98 443
40 % 56 102 452
30 % 56 102 469
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 255
95 % 54 95 346
90 % 54 95 358
70 % 54 97 383
50 % 71 171 278
40 % 71 171 291
30 % 71 170 320
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 50 91 304
95 % 57 98 347
90 % 57 98 359
70 % 57 99 392
50 % 74 156 328
40 % 74 158 335
30 % 74 158 350
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 94 260
95 % 54 94 351
90 % 54 94 363
70 % 54 95 398
50 % 71 178 265
40 % 72 179 271
30 % 140 251 199
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 31 67 492
95 % 54 90 372
90 % 54 91 381
70 % 72 171 253
50 % 74 175 263
40 % 74 175 280
30 % 74 175 301
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 93 269
95 % 53 93 364
90 % 53 93 377
70 % 53 94 410
50 % 69 161 315
40 % 70 168 304
30 % 70 168 325
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 258
95 % 54 95 350
90 % 54 95 361
70 % 54 96 396
50 % 54 96 453
40 % 54 96 481
30 % 54 96 510
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 86 294
95 % 54 86 397
90 % 54 87 407
70 % 70 162 264
50 % 72 169 284
40 % 72 170 293
30 % 72 170 317
Entity #2 | Chains: B
5S rRNA rna, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | Chains: R
60S ribosomal protein L43-A protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 86 295
95 % 54 86 399
90 % 54 86 415
70 % 54 87 447
50 % 71 169 283
40 % 72 170 294
30 % 94 193 249
Entity #21 | Chains: S
Ribosomal Protein uL1 protein, length: 217 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #22 | Chains: a
60S ribosomal protein L15-A protein, length: 204 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 97 246
95 % 55 99 329
90 % 55 99 340
70 % 71 168 259
50 % 73 182 248
40 % 73 182 262
30 % 73 182 283
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 48 87 293
95 % 48 87 393
90 % 54 94 362
70 % 54 95 397
50 % 71 170 280
40 % 71 171 289
30 % 71 171 314
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 98 239
95 % 53 98 331
90 % 53 99 335
70 % 53 99 379
50 % 71 180 251
40 % 71 180 268
30 % 71 180 288
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 253
95 % 54 95 344
90 % 54 96 350
70 % 54 96 390
50 % 70 171 287
40 % 70 176 285
30 % 70 176 309
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 89 282
95 % 51 89 383
90 % 51 89 399
70 % 51 91 425
50 % 69 169 289
40 % 69 170 298
30 % 69 170 321
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 93 267
95 % 53 93 363
90 % 53 94 374
70 % 53 94 406
50 % 69 161 318
40 % 70 162 321
30 % 70 163 334
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 89 276
95 % 54 89 373
90 % 54 90 385
70 % 54 90 426
50 % 70 160 319
40 % 70 166 315
30 % 72 173 306
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 38 68 432
95 % 38 68 585
90 % 38 68 612
70 % 38 68 655
50 % 38 68 688
40 % 38 68 713
30 % 39 69 720
Entity #3 | Chains: C
5.8S rRNA rna, length: 158 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #30 | Chains: i
60S ribosomal protein L23-A protein, length: 137 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 244
95 % 54 96 343
90 % 54 97 348
70 % 72 182 235
50 % 72 183 242
40 % 72 183 256
30 % 72 183 275
Entity #31 | Chains: j
60S ribosomal protein L24-A protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 63 437
95 % 40 63 590
90 % 40 63 619
70 % 40 63 659
50 % 40 63 695
40 % 44 105 480
30 % 44 105 509
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 73 400
95 % 39 73 527
90 % 39 73 556
70 % 39 73 591
50 % 39 73 630
40 % 39 75 652
30 % 39 76 681
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 100 234
95 % 54 100 320
90 % 54 101 328
70 % 54 101 371
50 % 71 180 250
40 % 71 180 267
30 % 71 180 287
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 284
95 % 53 89 385
90 % 53 90 389
70 % 53 90 431
50 % 69 156 331
40 % 70 169 299
30 % 71 171 318
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 87 296
95 % 54 90 371
90 % 54 91 380
70 % 54 91 417
50 % 71 173 272
40 % 72 174 284
30 % 72 176 300
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 81 314
95 % 53 81 419
90 % 53 82 437
70 % 53 82 481
50 % 53 82 508
40 % 53 82 538
30 % 53 82 566
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 249
95 % 56 95 342
90 % 56 96 347
70 % 56 96 388
50 % 74 179 252
40 % 74 179 270
30 % 74 179 290
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 93 263
95 % 54 93 355
90 % 54 93 368
70 % 54 94 399
50 % 71 170 281
40 % 71 170 296
30 % 71 170 319
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 243
95 % 54 96 341
90 % 54 96 352
70 % 54 97 387
50 % 72 174 266
40 % 72 178 273
30 % 72 179 293
Entity #4 | Chains: Y
Tyrosine-protein phosphatase YVH1 protein, length: 364 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 4 5 18677
95 % 4 5 16582
90 % 4 5 17066
70 % 4 5 15239
50 % 4 5 14410
40 % 4 5 12811
30 % 4 5 12206
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 94 264
95 % 53 94 358
90 % 53 94 372
70 % 53 95 400
50 % 69 166 303
40 % 70 168 311
30 % 70 168 330
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 290
95 % 53 89 389
90 % 53 89 406
70 % 53 90 439
50 % 69 155 334
40 % 69 155 345
30 % 69 155 359
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 99 235
95 % 54 99 321
90 % 54 99 331
70 % 54 100 373
50 % 70 172 285
40 % 71 183 254
30 % 72 185 266
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 90 280
95 % 53 94 357
90 % 53 94 371
70 % 53 95 402
50 % 53 95 456
40 % 70 163 318
30 % 70 173 311
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 247
95 % 54 96 339
90 % 54 96 353
70 % 58 132 311
50 % 71 178 258
40 % 71 178 274
30 % 71 178 295
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 288
95 % 53 89 384
90 % 53 89 401
70 % 53 90 430
50 % 53 90 472
40 % 54 97 471
30 % 54 97 497
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 92 271
95 % 54 92 367
90 % 54 92 376
70 % 70 161 269
50 % 71 174 269
40 % 71 176 278
30 % 72 177 298
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 31 1541
95 % 9 31 2061
90 % 10 54 1111
70 % 10 57 1070
50 % 10 57 1108
40 % 10 57 1140
30 % 10 57 1182
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 24926
95 % 3 4 21896
90 % 3 4 21259
70 % 3 4 19591
50 % 13 64 1061
40 % 13 64 1095
30 % 13 64 1133
Entity #5 | Chains: X
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 15 31 1714
95 % 15 31 2253
90 % 15 31 2308
70 % 16 32 2298
50 % 18 36 1825
40 % 18 36 1871
30 % 19 38 1739
Entity #6 | Chains: W
Large subunit GTPase 1 protein, length: 640 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 6 7 12692
95 % 6 7 12597
90 % 6 8 10793
70 % 6 8 10354
50 % 6 8 9575
40 % 6 8 9097
30 % 6 8 8459
Entity #7 | Chains: V
60S ribosomal export protein NMD3 protein, length: 518 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 11 7112
95 % 9 11 7731
90 % 9 11 7714
70 % 9 11 7446
50 % 9 11 7015
40 % 9 11 6889
30 % 9 11 6466
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 89 281
95 % 54 89 381
90 % 54 90 387
70 % 70 159 274
50 % 71 172 274
40 % 139 243 197
30 % 139 243 207
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 274
95 % 54 95 348
90 % 54 96 355
70 % 54 96 394
50 % 73 183 240
40 % 73 183 252
30 % 73 185 265

Instructions

In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.



View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB.

You can also use the structure comparison tool to compare any 2 given structures


ACTION - (A) Select for download / view details OR (B) Select two chains for comparison
Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 5DGE 81 m2 60S ribosomal protein L12-A 4932
2 4V7R 72 DL 60S ribosomal protein L12 4932
3 6R84 26 P 60S ribosomal protein L12-A 4932
4 6R86 25 P 60S ribosomal protein L12-A 4932
5 6R87 25 P 60S ribosomal protein L12-A 4932
6 6R7Q 75 t uL11 9986
7 6R6G 79 t uL11 9986
8 6R6P 47 t Ribosomal protein L12 9986
9 6R5Q 50 t uL11 9986
10 6QKL 11 D 60S ribosomal protein L12 44689
11 6N8J 44 K 60S ribosomal protein L12 4932
12 6N8M 46 L Ribosomal protein L12 4932
13 6N8N 48 L Ribosomal protein L12 4932
14 6N8O 6 L Ribosomal protein L12 4932
15 6MTD 47 t eL11 9986
16 6MTE 47 t uL11 9986
17 6HCQ 81 u3 Ribosomal protein L12 9986
18 6HCJ 81 u3 Ribosomal protein L12 9986
19 6HCM 79 t3 Ribosomal protein L12 9986
20 6HCF 79 t3 Ribosomal protein L12 9986
21 6GZ3 84 Aq Ribosomal protein L12 9986
22 6GZ4 84 Aq ribosomal protein uL11 9986
23 6GZ5 84 Aq ribosomal protein uL11 9986
24 6FTG 44 t Ribosomal protein L12 9986
25 6FTI 44 t Ribosomal protein L12 9986
26 6FTJ 44 t Ribosomal protein L12 9986
27 6FRK 4 4 Ribosomal protein L12 9986
28 5LZS 44 t uL11 9986
29 5LZT 44 t uL11 9986
30 5LZU 44 t uL11 9986
31 5LZV 44 t uL11 9986
32 5LZW 44 t uL11 9986
33 5LZX 44 t uL11 9986
34 5LZY 44 t uL11 9986
35 5LZZ 44 t uL11 9986
36 5JUO 16 P uL11 (yeast L12) 4932
37 5JUP 16 P uL11 (yeast L12) 4932
38 5JUS 16 P uL11 (yeast L12) 4932
39 5JUT 16 P uL11 (yeast L12) 4932
40 5JUU 16 P uL11 (yeast L12) 4932
41 5JCS 21 K 60S ribosomal protein L12-A 4932
42 5FL8 11 K 60S ribosomal protein L12-A 4932
43 5AN9 4 D 60S RIBOSOMAL PROTEIN L12 44689
44 5ANB 4 D 60S RIBOSOMAL PROTEIN L12 44689
45 5ANC 4 D 60S RIBOSOMAL PROTEIN L12 44689
46 5A8L 4 G 60S RIBOSOMAL PROTEIN L12 9606
47 3JAN 46 K Ribosomal protein uL11 SEE REMARK 999 9986
48 3JAJ 46 K Ribosomal protein uL11 SEE REMARK 999 9986
49 3JAG 44 t uL11 9986
50 3JAH 44 t uL11 9986
51 3JAI 44 t uL11 9986
52 5AJ0 45 Aq 60S ribosomal protein L12 9606
53 3J92 43 t uL11 9986
54 3J7P 14 K Ribosomal protein uL11 9823
55 3J77 12 62 60S ribosomal protein L12 4932
56 3J78 12 62 60S ribosomal protein L12 4932
57 4V7F 12 I 60S ribosomal protein L12 4932
58 4V7E 65 CK 60S ribosomal protein L11 4565
59 4V6W 40 CK 60S ribosomal protein L12 7227
60 4V6X 40 CK 60S ribosomal protein L12 9606
61 4V8M 46 BM 60S RIBOSOMAL PROTEIN L12, PUTATIVE 185431
62 3J16 10 H 60S ribosomal protein L11 4932
63 4V6I 39 BJ 60S ribosomal protein rpL12 (L11p) 4932
64 4V5Z 61 Bi 60S Ribosomal protein L12 9612