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 93 253
95 % 52 97 324
90 % 52 97 336
70 % 52 98 375
50 % 65 141 339
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 83 297
95 % 52 85 388
90 % 52 85 406
70 % 52 86 435
50 % 65 162 288
40 % 66 164 293
30 % 66 164 309
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 93 252
95 % 52 93 341
90 % 52 94 348
70 % 52 95 385
50 % 53 96 438
40 % 54 100 448
30 % 54 100 467
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 93 256
95 % 52 93 347
90 % 52 93 360
70 % 52 95 387
50 % 65 165 276
40 % 65 165 292
30 % 65 164 316
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 89 303
95 % 55 96 344
90 % 55 96 358
70 % 55 97 391
50 % 68 150 328
40 % 68 152 341
30 % 68 152 353
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 92 260
95 % 52 92 354
90 % 52 92 367
70 % 52 93 401
50 % 65 172 265
40 % 66 173 268
30 % 134 245 203
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 65 485
95 % 52 88 373
90 % 52 89 385
70 % 66 165 248
50 % 68 169 263
40 % 68 169 279
30 % 68 169 300
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 91 265
95 % 51 91 363
90 % 51 91 375
70 % 51 92 413
50 % 51 92 463
40 % 64 162 305
30 % 64 162 323
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 93 254
95 % 52 93 343
90 % 52 93 357
70 % 52 94 390
50 % 52 94 453
40 % 52 94 478
30 % 52 94 509
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 84 295
95 % 52 84 394
90 % 52 85 408
70 % 64 151 273
50 % 66 163 284
40 % 65 163 299
30 % 66 164 314
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 84 293
95 % 52 84 393
90 % 52 84 411
70 % 52 85 443
50 % 65 163 281
40 % 66 164 296
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 95 245
95 % 53 97 328
90 % 53 97 341
70 % 65 162 252
50 % 67 176 244
40 % 67 176 259
30 % 134 246 202
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 85 389
90 % 52 92 363
70 % 52 93 399
50 % 65 164 279
40 % 65 165 290
30 % 65 165 307
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 96 240
95 % 51 96 331
90 % 51 97 337
70 % 51 97 380
50 % 65 174 250
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 93 258
95 % 52 93 350
90 % 52 94 350
70 % 52 94 389
50 % 64 165 290
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 88 275
95 % 50 88 372
90 % 50 88 390
70 % 50 90 420
50 % 64 164 283
40 % 64 165 298
30 % 64 165 315
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 91 362
90 % 51 92 369
70 % 51 92 411
50 % 63 155 320
40 % 64 156 325
30 % 64 157 336
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 87 284
95 % 52 87 378
90 % 52 88 391
70 % 52 88 429
50 % 64 154 321
40 % 64 160 320
30 % 66 167 303
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 67 418
95 % 37 67 564
90 % 37 67 587
70 % 37 67 622
50 % 37 67 661
40 % 37 67 687
30 % 38 68 696
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 94 248
95 % 52 94 336
90 % 52 95 347
70 % 66 176 235
50 % 66 177 239
40 % 66 177 253
30 % 66 177 272
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 62 422
95 % 39 62 572
90 % 39 62 592
70 % 39 62 640
50 % 39 62 676
40 % 39 100 491
30 % 39 100 518
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 38 72 394
95 % 38 72 514
90 % 38 72 544
70 % 38 72 579
50 % 38 72 607
40 % 38 74 624
30 % 38 75 653
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 98 320
90 % 52 99 328
70 % 52 99 370
50 % 65 174 249
40 % 65 174 266
30 % 65 174 284
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 87 287
95 % 51 87 386
90 % 51 88 397
70 % 51 88 434
50 % 63 150 329
40 % 64 163 301
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 85 292
95 % 52 88 371
90 % 52 89 379
70 % 52 89 423
50 % 65 167 270
40 % 66 168 285
30 % 66 170 299
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 79 306
95 % 51 79 412
90 % 51 80 434
70 % 51 80 464
50 % 51 80 501
40 % 51 80 532
30 % 51 80 562
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 93 247
95 % 54 93 335
90 % 54 94 345
70 % 54 94 386
50 % 67 134 350
40 % 67 134 369
30 % 67 134 380
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 91 263
95 % 52 91 359
90 % 52 91 372
70 % 52 92 407
50 % 65 164 280
40 % 65 164 295
30 % 65 164 312
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 94 250
95 % 52 94 340
90 % 52 94 355
70 % 52 95 388
50 % 66 168 268
40 % 66 172 273
30 % 66 173 288
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 18161
95 % 4 5 16983
90 % 4 5 16686
70 % 4 5 15620
50 % 4 5 14091
40 % 4 5 13106
30 % 4 5 11911
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 92 262
95 % 51 92 357
90 % 51 92 370
70 % 51 93 405
50 % 63 160 304
40 % 64 162 315
30 % 64 162 332
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 87 385
90 % 51 87 403
70 % 51 88 432
50 % 63 149 331
40 % 63 149 349
30 % 63 149 360
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 97 234
95 % 52 97 327
90 % 52 97 339
70 % 52 98 376
50 % 64 166 286
40 % 65 177 251
30 % 66 179 267
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 88 286
95 % 51 92 360
90 % 51 92 373
70 % 51 93 408
50 % 51 93 461
40 % 64 157 322
30 % 64 157 339
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 94 249
95 % 52 94 339
90 % 52 94 354
70 % 52 126 318
50 % 65 172 256
40 % 65 172 271
30 % 65 172 290
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 87 382
90 % 51 87 405
70 % 51 88 433
50 % 51 88 477
40 % 52 95 467
30 % 52 95 495
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 90 266
95 % 52 90 364
90 % 52 90 376
70 % 64 156 266
50 % 65 168 267
40 % 65 170 277
30 % 66 171 295
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 1590
95 % 8 30 2102
90 % 9 53 1096
70 % 9 56 1052
50 % 9 56 1089
40 % 9 56 1128
30 % 9 56 1165
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 23415
95 % 3 4 20711
90 % 3 4 20216
70 % 3 4 18663
50 % 12 63 1052
40 % 12 63 1091
30 % 12 63 1125
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 1755
95 % 14 30 2315
90 % 14 30 2379
70 % 15 31 2268
50 % 17 35 1788
40 % 17 35 1842
30 % 18 37 1720
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 12532
95 % 6 7 12408
90 % 6 8 10839
70 % 6 8 10420
50 % 6 8 9604
40 % 6 8 9133
30 % 6 8 8467
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 6973
95 % 9 11 7625
90 % 9 11 7596
70 % 9 11 7429
50 % 9 11 7019
40 % 9 11 6786
30 % 9 11 6375
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 87 281
95 % 52 87 379
90 % 52 88 388
70 % 64 153 269
50 % 65 166 272
40 % 133 237 197
30 % 133 237 206
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 50 91 271
95 % 52 93 346
90 % 52 94 352
70 % 52 94 393
50 % 67 177 236
40 % 67 177 250
30 % 67 179 266

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 4V88 76 Bm, Dm 60S ribosomal protein L40 4932
2 6HHQ 41 AN, DO Ubiquitin-60S ribosomal protein L40 4932
3 4V8P 10 AK, DK, FK, HK UBIQUITIN-60S RIBOSOMAL PROTEIN L40 5911
4 6RI5 46 t Ubiquitin-60S ribosomal protein L40 4932
5 6QTZ 46 t Ubiquitin-60S ribosomal protein L40 4932
6 6QT0 41 t Ubiquitin-60S ribosomal protein L40 4932
7 6QIK 45 t Ubiquitin-60S ribosomal protein L40 4932
8 6N8M 44 z Ubiquitin-60S ribosomal protein L40 4932
9 6N8N 47 z Ubiquitin-60S ribosomal protein L40 4932
10 6N8O 49 z Ubiquitin-60S ribosomal protein L40 4932
11 6IP5 41 2g Ubiquitin-60S ribosomal protein L40 9606
12 6IP6 41 2g Ubiquitin-60S ribosomal protein L40 9606
13 6IP8 41 2g Ubiquitin-60S ribosomal protein L40 9606
14 6HD7 44 o Ubiquitin-60S ribosomal protein L40 4932
15 6EF3 24 u Ubiquitin-60S ribosomal protein L40 4932
16 6EK0 41 Lm Ubiquitin-60S ribosomal protein L40 Modified amino acid MLZ (Methyl-lysine) 9606
17 5XXB 41 l Ribosomal protein eL40 5811
18 5UMD 42 f Ubiquitin-60S ribosomal protein L40 5833
19 5MC6 55 AO Ubiquitin-60S ribosomal protein L40 4932
20 5T62 42 z Ubiquitin-60S ribosomal protein L40 4932
21 5T6R 41 z Ubiquitin-60S ribosomal protein L40 4932
22 5T2C 27 g Ubiquitin-60S ribosomal protein L40 9606
23 5LKS 41 Lm Ubiquitin-60S ribosomal protein L40 9606
24 5JUO 44 RA eL40 (yeast L40) 4932
25 5JUP 44 RA eL40 (yeast L40) 4932
26 5JUS 44 RA eL40 (yeast L40) 4932
27 5JUT 44 RA eL40 (yeast L40) 4932
28 5JUU 44 RA eL40 (yeast L40) 4932
29 5GAK 36 o Ubiquitin-60S ribosomal protein L40 4932
30 5APN 41 m Ubiquitin-60S ribosomal protein L40 4932
31 5APO 41 m Ubiquitin-60S ribosomal protein L40 4932
32 4UG0 41 Lm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9606
33 5AJ0 41 Am Ubiquitin-60S ribosomal protein L40 9606
34 3J92 38 m eL40 9986
35 4D67 38 m UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
36 4D5Y 38 m 60S RIBOSOMAL PROTEIN EL40 9986
37 3J7O 41 m Ribosomal protein eL40 9823
38 3J7P 42 m Ribosomal protein eL40 9823
39 3J7Q 41 m Ribosomal protein eL40 9823
40 3J7R 41 m Ribosomal protein eL40 9823
41 4UJC 44 Bm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
42 4UJD 41 Am UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
43 3J79 42 f 60S ribosomal protein eL40 5833
44 3J77 40 90 60S ribosomal protein L40 4932
45 3J78 40 90 60S ribosomal protein L40 4932
46 3J6X 42 80 60S ribosomal protein L40 4932
47 3J6Y 42 80 60S ribosomal protein L40 4932
48 4UJE 75 Cm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
49 4V91 41 m EL40 RIBOSOMAL PROTEIN EL40 28985
50 4V8Y 73 Bm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 4932
51 4V8Z 73 Bm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 4932
52 4V8T 39 m 60S RIBOSOMAL PROTEIN L40 4932
53 4ADX 6 5 RPL40E 145262