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 % 52 93 256
95 % 52 97 326
90 % 52 97 339
70 % 52 98 375
50 % 65 141 338
40 % 66 177 255
30 % 66 177 274
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 83 299
95 % 52 85 390
90 % 52 85 409
70 % 52 86 436
50 % 65 162 289
40 % 66 164 293
30 % 66 164 311
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 257
95 % 52 93 352
90 % 52 94 357
70 % 52 95 388
50 % 53 96 442
40 % 54 100 448
30 % 54 100 470
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 252
95 % 52 93 343
90 % 52 93 359
70 % 52 95 384
50 % 65 165 275
40 % 65 165 292
30 % 65 164 318
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 48 89 304
95 % 55 96 345
90 % 55 96 361
70 % 55 97 389
50 % 68 150 328
40 % 68 152 342
30 % 68 152 355
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 92 258
95 % 52 92 354
90 % 52 92 368
70 % 52 93 402
50 % 65 172 265
40 % 66 174 268
30 % 134 245 202
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 29 65 482
95 % 52 88 375
90 % 52 89 384
70 % 66 165 248
50 % 68 169 263
40 % 68 169 280
30 % 68 169 302
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 91 266
95 % 51 91 364
90 % 51 91 379
70 % 51 92 415
50 % 51 92 464
40 % 64 162 308
30 % 64 162 327
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 255
95 % 52 93 348
90 % 52 93 363
70 % 52 94 392
50 % 52 94 452
40 % 52 94 480
30 % 52 94 508
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 84 293
95 % 52 84 392
90 % 52 85 408
70 % 64 151 272
50 % 66 163 282
40 % 65 163 299
30 % 66 164 315
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 % 52 84 296
95 % 52 84 395
90 % 52 84 413
70 % 52 85 442
50 % 65 163 281
40 % 66 164 295
30 % 88 187 253
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 % 52 95 244
95 % 53 97 328
90 % 53 97 341
70 % 65 162 253
50 % 67 176 245
40 % 67 176 262
30 % 67 176 281
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 46 85 291
95 % 46 85 391
90 % 52 92 367
70 % 52 93 398
50 % 65 164 277
40 % 65 165 290
30 % 65 165 309
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 96 237
95 % 51 96 331
90 % 51 97 338
70 % 51 97 379
50 % 65 174 249
40 % 65 174 267
30 % 65 174 285
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 253
95 % 52 93 347
90 % 52 94 353
70 % 52 94 391
50 % 64 165 287
40 % 64 170 288
30 % 64 170 305
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 50 88 276
95 % 50 88 374
90 % 50 88 392
70 % 50 90 419
50 % 64 164 280
40 % 64 165 298
30 % 64 165 317
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 91 267
95 % 51 91 365
90 % 51 92 376
70 % 51 92 418
50 % 63 155 325
40 % 64 156 328
30 % 64 157 342
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 87 283
95 % 52 87 379
90 % 52 88 393
70 % 52 88 427
50 % 64 154 322
40 % 64 160 321
30 % 66 167 306
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 37 67 417
95 % 37 67 558
90 % 37 67 588
70 % 37 67 628
50 % 37 67 665
40 % 37 67 693
30 % 38 68 697
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 % 52 94 245
95 % 52 94 336
90 % 52 95 347
70 % 66 176 235
50 % 66 177 240
40 % 66 177 256
30 % 66 177 275
Entity #31 | Chains: j
60S ribosomal protein L24-A protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 62 419
95 % 39 62 571
90 % 39 62 596
70 % 39 62 635
50 % 39 62 678
40 % 39 100 490
30 % 39 100 514
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 38 72 392
95 % 38 72 518
90 % 38 72 541
70 % 38 72 572
50 % 38 72 605
40 % 38 74 623
30 % 38 75 650
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 98 232
95 % 52 98 322
90 % 52 99 330
70 % 52 99 372
50 % 65 171 259
40 % 65 171 276
30 % 65 171 298
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 87 289
95 % 51 87 385
90 % 51 88 397
70 % 51 88 434
50 % 63 150 329
40 % 64 163 302
30 % 65 165 313
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 85 295
95 % 52 88 373
90 % 52 89 380
70 % 52 89 425
50 % 65 167 269
40 % 66 168 286
30 % 66 170 300
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 79 308
95 % 51 79 413
90 % 51 80 435
70 % 51 80 466
50 % 51 80 499
40 % 51 80 531
30 % 51 80 556
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 93 248
95 % 54 93 341
90 % 54 94 348
70 % 54 94 387
50 % 67 134 351
40 % 67 134 370
30 % 67 134 381
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 91 262
95 % 52 91 360
90 % 52 91 371
70 % 52 92 408
50 % 65 164 278
40 % 65 164 297
30 % 65 164 316
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 94 246
95 % 52 94 337
90 % 52 94 351
70 % 52 95 386
50 % 66 168 266
40 % 66 172 270
30 % 66 173 289
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 17191
95 % 4 5 16914
90 % 4 5 16653
70 % 4 5 14908
50 % 4 5 14049
40 % 4 5 13052
30 % 4 5 11413
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 92 261
95 % 51 92 358
90 % 51 92 373
70 % 51 93 406
50 % 63 160 306
40 % 64 162 316
30 % 64 162 334
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 87 288
95 % 51 87 388
90 % 51 87 407
70 % 51 88 432
50 % 63 149 332
40 % 63 149 349
30 % 63 149 362
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 97 235
95 % 52 97 327
90 % 52 97 340
70 % 52 98 373
50 % 64 166 285
40 % 65 177 252
30 % 66 179 269
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 88 281
95 % 51 92 361
90 % 51 92 372
70 % 51 93 409
50 % 51 93 461
40 % 64 157 323
30 % 64 167 307
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 94 247
95 % 52 94 335
90 % 52 94 350
70 % 52 126 318
50 % 65 172 255
40 % 65 172 273
30 % 65 172 293
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 87 290
95 % 51 87 389
90 % 51 87 405
70 % 51 88 433
50 % 51 88 477
40 % 52 95 468
30 % 52 95 494
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 90 265
95 % 52 90 363
90 % 52 90 377
70 % 64 156 267
50 % 65 168 268
40 % 65 170 278
30 % 66 171 296
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 8 30 1588
95 % 8 30 2078
90 % 9 53 1096
70 % 9 56 1050
50 % 9 56 1089
40 % 9 56 1130
30 % 9 56 1174
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 22190
95 % 3 4 23869
90 % 3 4 19503
70 % 3 4 21208
50 % 12 63 1052
40 % 12 63 1092
30 % 12 63 1130
Entity #5 | Chains: X
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 14 30 1696
95 % 14 30 2250
90 % 14 30 2303
70 % 15 31 2290
50 % 17 35 1785
40 % 17 35 1844
30 % 18 37 1725
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 12517
95 % 6 7 12428
90 % 6 8 11143
70 % 6 8 10484
50 % 6 8 9646
40 % 6 8 9141
30 % 6 8 8469
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 6930
95 % 9 11 7546
90 % 9 11 7538
70 % 9 11 7389
50 % 9 11 6959
40 % 9 11 6734
30 % 9 11 6319
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 87 286
95 % 52 87 376
90 % 52 88 390
70 % 64 153 269
50 % 65 166 271
40 % 133 237 197
30 % 133 237 205
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 50 91 270
95 % 52 93 350
90 % 52 94 356
70 % 52 94 396
50 % 67 177 238
40 % 67 177 251
30 % 67 179 268

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