6N8J

Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit


Sequence Similarity Clusters for the Entities in PDB 6N8J

Entity #1 | Chains: D
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 75 306
95 % 40 77 402
90 % 40 77 423
70 % 40 78 454
50 % 49 150 312
40 % 49 150 323
30 % 49 150 339
Entity #10 | Chains: E
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 85 267
95 % 40 85 360
90 % 40 86 369
70 % 40 87 407
50 % 41 88 459
40 % 42 92 471
30 % 42 92 496
Entity #11 | Chains: e
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 86 263
95 % 40 86 355
90 % 40 86 370
70 % 40 87 410
50 % 49 155 289
40 % 49 159 290
30 % 49 160 301
Entity #12 | Chains: F
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 85 269
95 % 40 85 362
90 % 40 85 377
70 % 40 87 408
50 % 49 153 302
40 % 49 153 313
30 % 49 152 328
Entity #13 | Chains: f
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 84 276
95 % 39 84 376
90 % 39 84 391
70 % 39 85 428
50 % 47 148 323
40 % 47 149 336
30 % 47 149 350
Entity #14 | Chains: G
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 36 81 312
95 % 43 88 363
90 % 43 88 378
70 % 43 89 416
50 % 52 138 346
40 % 52 140 359
30 % 52 140 369
Entity #15 | Chains: g
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 79 290
95 % 39 79 396
90 % 39 79 415
70 % 39 80 444
50 % 47 137 348
40 % 47 137 367
30 % 47 137 377
Entity #16 | Chains: I
Bud site selection protein 20 protein, length: 166 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 5 17096
95 % 1 5 16045
90 % 1 5 15828
70 % 1 5 14829
50 % 1 5 13405
40 % 1 5 12473
30 % 1 5 11341
Entity #17 | Chains: H
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 84 272
95 % 40 84 370
90 % 40 84 385
70 % 40 85 422
50 % 49 160 278
40 % 50 162 281
30 % 117 232 206
Entity #18 | Chains: h
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 89 251
95 % 40 89 346
90 % 40 89 358
70 % 40 90 401
50 % 48 154 309
40 % 49 165 268
30 % 49 166 283
Entity #19 | Chains: i
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 80 286
95 % 39 84 375
90 % 39 84 390
70 % 39 85 427
50 % 39 85 479
40 % 48 145 340
30 % 48 145 356
Entity #2 | Chains: J
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 17 57 545
95 % 40 80 386
90 % 40 81 401
70 % 50 153 263
50 % 51 156 283
40 % 51 156 301
30 % 51 156 315
Entity #20 | Chains: j
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 86 262
95 % 40 86 357
90 % 40 86 375
70 % 40 118 325
50 % 49 160 272
40 % 49 160 289
30 % 49 160 304
Entity #21 | Chains: k
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 79 292
95 % 39 79 398
90 % 39 79 416
70 % 39 80 448
50 % 39 80 494
40 % 40 87 492
30 % 40 87 519
Entity #22 | Chains: m
Nucleolar GTP-binding protein 2 protein, length: 486 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 3 34647
95 % 1 3 28722
90 % 1 3 27689
70 % 1 3 25139
50 % 1 3 22078
40 % 1 3 20218
30 % 1 3 18088
Entity #23 | Chains: L
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 83 282
95 % 39 83 380
90 % 39 83 395
70 % 39 84 431
50 % 47 143 336
40 % 48 150 327
30 % 48 150 340
Entity #24 | Chains: l
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 82 281
95 % 40 82 379
90 % 40 82 393
70 % 48 143 279
50 % 49 156 285
40 % 49 158 295
30 % 49 158 309
Entity #25 | Chains: M
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 85 270
95 % 40 85 365
90 % 40 85 379
70 % 40 86 419
50 % 40 86 476
40 % 40 86 506
30 % 40 86 527
Entity #26 | Chains: p
60S ribosomal protein L43-A protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 76 300
95 % 40 76 412
90 % 40 76 433
70 % 40 77 460
50 % 49 151 307
40 % 49 151 318
30 % 71 174 269
Entity #27 | Chains: N
60S ribosomal protein L15-A protein, length: 204 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 87 259
95 % 41 89 348
90 % 41 89 361
70 % 49 150 266
50 % 50 163 264
40 % 117 233 197
30 % 117 233 204
Entity #28 | Chains: u
Ribosome biogenesis protein RLP24 protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 13 5054
95 % 1 13 5854
90 % 1 13 5891
70 % 1 13 5821
50 % 1 13 5606
40 % 1 13 5465
30 % 1 13 5196
Entity #29 | Chains: O
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 83 274
95 % 40 83 374
90 % 40 84 383
70 % 40 85 421
50 % 49 152 305
40 % 49 153 310
30 % 49 153 325
Entity #3 | Chains: A
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 79 289
95 % 40 79 395
90 % 40 80 404
70 % 48 141 287
50 % 49 154 294
40 % 116 224 204
30 % 116 224 211
Entity #30 | Chains: P
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 89 245
95 % 40 89 338
90 % 40 90 347
70 % 40 90 396
50 % 49 162 265
40 % 49 162 279
30 % 49 162 296
Entity #31 | Chains: Q
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 85 266
95 % 40 85 361
90 % 40 86 371
70 % 40 86 412
50 % 48 153 313
40 % 48 158 303
30 % 48 158 319
Entity #32 | Chains: R
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 82 277
95 % 40 82 377
90 % 40 82 392
70 % 40 84 423
50 % 50 154 298
40 % 50 155 307
30 % 50 155 323
Entity #33 | Chains: r
Ribosome biogenesis protein NSA2 protein, length: 261 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 6 14535
95 % 1 6 14735
90 % 1 6 14544
70 % 1 6 13724
50 % 1 6 12473
40 % 1 6 11638
30 % 1 6 10629
Entity #34 | Chains: S
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 83 280
95 % 39 83 378
90 % 39 84 389
70 % 39 84 430
50 % 47 143 335
40 % 48 144 342
30 % 48 145 353
Entity #35 | Chains: T
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 79 287
95 % 40 79 391
90 % 40 80 402
70 % 40 80 442
50 % 48 142 333
40 % 48 148 338
30 % 49 154 322
Entity #36 | Chains: U
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 27 61 438
95 % 27 61 596
90 % 27 61 623
70 % 27 61 661
50 % 27 61 702
40 % 27 61 738
30 % 28 62 748
Entity #37 | Chains: V
60S ribosomal protein L23-A protein, length: 137 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 86 260
95 % 40 86 356
90 % 40 87 363
70 % 50 164 243
50 % 50 165 257
40 % 50 165 267
30 % 50 165 287
Entity #38 | Chains: W
Ribosome assembly factor MRT4 protein, length: 236 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 11 6644
95 % 1 11 7253
90 % 1 11 7250
70 % 1 11 7112
50 % 1 11 6717
40 % 1 11 6502
30 % 1 11 6086
Entity #39 | Chains: X
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 28 66 409
95 % 28 66 549
90 % 28 66 571
70 % 28 66 610
50 % 28 66 652
40 % 28 68 665
30 % 28 69 697
Entity #4 | Chains: a
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 77 299
95 % 40 80 385
90 % 40 81 396
70 % 40 81 436
50 % 49 155 293
40 % 49 155 306
30 % 49 157 314
Entity #40 | Chains: Y
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 90 244
95 % 40 90 337
90 % 40 91 343
70 % 40 91 393
50 % 49 159 275
40 % 49 159 292
30 % 49 159 307
Entity #41 | Chains: y
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 2 22 2583
95 % 2 22 3228
90 % 2 22 3302
70 % 3 23 3186
50 % 5 27 2332
40 % 5 27 2360
30 % 6 29 2147
Entity #42 | Chains: Z
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 79 291
95 % 39 79 397
90 % 39 80 406
70 % 39 80 445
50 % 47 138 347
40 % 48 151 322
30 % 48 152 336
Entity #43 | Chains: z
UPF0642 protein YBL028C protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 8 10847
95 % 1 8 10936
90 % 1 8 10832
70 % 1 8 10417
50 % 1 8 9595
40 % 1 8 9105
30 % 1 8 8403
Entity #44 | Chains: K
60S ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 4 27651
95 % 1 4 23699
90 % 1 4 19327
70 % 1 4 21094
50 % 4 57 1159
40 % 4 57 1192
30 % 4 57 1232
Entity #45 | Chains: q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 76 301
95 % 40 76 413
90 % 40 77 428
70 % 48 139 291
50 % 49 150 314
40 % 49 151 320
30 % 49 151 335
Entity #46 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 71 321
95 % 39 71 435
90 % 39 72 461
70 % 39 72 493
50 % 39 72 526
40 % 39 72 567
30 % 39 72 595
Entity #47 | Chains: 1
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 #48 | Chains: 2
5S rRNA rna, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #49 | Chains: 3
5.8S rRNA rna, length: 158 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #5 | Chains: B
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 38 83 285
95 % 40 85 364
90 % 40 86 374
70 % 40 86 417
50 % 50 164 259
40 % 50 164 273
30 % 50 166 280
Entity #6 | Chains: b
Nucleolar GTP-binding protein 1 protein, length: 647 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 12 6164
95 % 1 12 6870
90 % 1 12 6883
70 % 1 12 6768
50 % 1 12 6436
40 % 1 12 6238
30 % 1 12 5879
Entity #7 | Chains: C
60S ribosomal protein L4-A protein, length: 362 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 85 268
95 % 40 89 342
90 % 40 89 353
70 % 40 90 397
50 % 49 129 357
40 % 49 164 271
30 % 49 164 289
Entity #8 | Chains: c
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 42 85 261
95 % 42 85 359
90 % 42 86 367
70 % 42 86 409
50 % 52 161 266
40 % 52 161 280
30 % 52 161 297
Entity #9 | Chains: d
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 83 275
95 % 40 83 372
90 % 40 83 388
70 % 40 84 426
50 % 49 152 304
40 % 49 152 314
30 % 49 152 327

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