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 95 265
95 % 54 99 331
90 % 54 99 344
70 % 54 100 381
50 % 71 147 341
40 % 72 183 257
30 % 72 183 277
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 85 311
95 % 54 87 400
90 % 54 87 420
70 % 54 88 450
50 % 71 168 291
40 % 72 170 294
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 95 264
95 % 54 95 355
90 % 54 96 361
70 % 54 97 392
50 % 55 98 447
40 % 56 102 458
30 % 56 102 473
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 95 267
95 % 54 95 358
90 % 54 95 372
70 % 54 97 395
50 % 71 171 281
40 % 71 171 293
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 91 313
95 % 57 98 354
90 % 57 98 370
70 % 57 99 402
50 % 74 156 329
40 % 74 158 337
30 % 74 158 352
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 94 272
95 % 54 94 359
90 % 54 94 373
70 % 54 95 403
50 % 71 178 264
40 % 72 179 272
30 % 140 251 200
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 67 500
95 % 54 90 380
90 % 54 91 393
70 % 72 171 255
50 % 74 175 265
40 % 74 175 281
30 % 74 175 302
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 93 280
95 % 53 93 370
90 % 53 93 385
70 % 53 94 415
50 % 53 94 464
40 % 70 168 305
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 95 269
95 % 54 95 353
90 % 54 95 371
70 % 54 96 399
50 % 54 96 459
40 % 54 96 487
30 % 54 96 518
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 86 307
95 % 54 86 408
90 % 54 87 423
70 % 70 157 281
50 % 72 169 287
40 % 71 169 298
30 % 72 170 319
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 86 306
95 % 54 86 407
90 % 54 86 427
70 % 54 87 458
50 % 71 169 285
40 % 72 170 297
30 % 94 193 250
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 97 255
95 % 55 99 333
90 % 55 99 350
70 % 71 168 265
50 % 73 182 251
40 % 73 182 264
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 87 301
95 % 48 87 403
90 % 54 94 376
70 % 54 95 404
50 % 71 170 284
40 % 71 171 290
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 98 250
95 % 53 98 334
90 % 53 99 343
70 % 53 99 384
50 % 71 180 254
40 % 71 180 271
30 % 71 180 291
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 95 266
95 % 54 95 357
90 % 54 96 364
70 % 54 96 400
50 % 70 171 292
40 % 70 176 287
30 % 70 176 311
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 89 288
95 % 51 89 383
90 % 51 89 400
70 % 51 91 423
50 % 69 169 289
40 % 69 170 299
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 93 277
95 % 53 93 372
90 % 53 94 379
70 % 53 94 413
50 % 69 161 318
40 % 70 162 322
30 % 70 163 335
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 89 290
95 % 54 89 388
90 % 54 90 397
70 % 54 90 433
50 % 70 160 319
40 % 70 166 316
30 % 72 173 309
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 68 438
95 % 38 68 593
90 % 38 68 624
70 % 38 68 665
50 % 38 68 693
40 % 38 68 718
30 % 39 69 730
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 96 256
95 % 54 96 348
90 % 54 97 357
70 % 72 182 238
50 % 72 183 245
40 % 72 183 256
30 % 72 183 276
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 63 444
95 % 40 63 605
90 % 40 63 634
70 % 40 63 675
50 % 40 63 702
40 % 44 105 489
30 % 44 105 517
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 73 412
95 % 39 73 540
90 % 39 73 568
70 % 39 73 602
50 % 39 73 638
40 % 39 75 657
30 % 39 76 687
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 100 244
95 % 54 100 326
90 % 54 101 336
70 % 54 101 375
50 % 71 180 253
40 % 71 180 268
30 % 71 180 289
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 89 294
95 % 53 89 393
90 % 53 90 405
70 % 53 90 439
50 % 69 156 332
40 % 70 169 300
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 87 305
95 % 54 90 379
90 % 54 91 392
70 % 54 91 422
50 % 71 173 275
40 % 72 174 285
30 % 72 176 301
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 81 323
95 % 53 81 428
90 % 53 82 448
70 % 53 82 483
50 % 53 82 513
40 % 53 82 548
30 % 53 82 569
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 253
95 % 56 95 343
90 % 56 96 352
70 % 56 96 389
50 % 69 136 360
40 % 69 136 377
30 % 69 136 386
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 93 275
95 % 54 93 364
90 % 54 93 382
70 % 54 94 407
50 % 71 170 283
40 % 71 170 296
30 % 71 170 317
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 261
95 % 54 96 346
90 % 54 96 359
70 % 54 97 394
50 % 72 174 271
40 % 72 178 277
30 % 72 179 294
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 19464
95 % 4 5 17627
90 % 4 5 17317
70 % 4 5 16143
50 % 4 5 14543
40 % 4 5 13532
30 % 4 5 12308
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 94 273
95 % 53 94 363
90 % 53 94 378
70 % 53 95 405
50 % 69 166 308
40 % 70 168 313
30 % 70 168 331
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 89 297
95 % 53 89 397
90 % 53 89 417
70 % 53 90 443
50 % 69 155 334
40 % 69 155 344
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 99 245
95 % 54 99 327
90 % 54 99 340
70 % 54 100 378
50 % 70 172 286
40 % 71 183 255
30 % 72 185 269
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 90 285
95 % 53 94 368
90 % 53 94 383
70 % 53 95 411
50 % 53 95 463
40 % 70 163 320
30 % 70 163 338
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 96 257
95 % 54 96 349
90 % 54 96 365
70 % 58 132 318
50 % 71 178 259
40 % 71 178 275
30 % 71 178 297
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 298
95 % 53 89 396
90 % 53 89 416
70 % 53 90 442
50 % 53 90 481
40 % 54 97 482
30 % 54 97 500
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 92 281
95 % 54 92 371
90 % 54 92 386
70 % 70 162 269
50 % 71 174 269
40 % 71 176 279
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 1583
95 % 9 31 2066
90 % 10 54 1130
70 % 10 57 1086
50 % 10 57 1125
40 % 10 57 1154
30 % 10 57 1194
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 27641
95 % 3 4 22273
90 % 3 4 18423
70 % 3 4 18090
50 % 13 64 1075
40 % 13 64 1111
30 % 13 64 1145
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 1722
95 % 15 31 2236
90 % 15 31 2289
70 % 16 32 2265
50 % 18 36 1807
40 % 18 36 1861
30 % 19 38 1752
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 12729
95 % 6 7 13024
90 % 6 8 11070
70 % 6 8 11125
50 % 6 8 10109
40 % 6 8 9293
30 % 6 8 8857
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 7334
95 % 9 11 7851
90 % 9 11 7851
70 % 9 11 7672
50 % 9 11 7301
40 % 9 11 7046
30 % 9 11 6534
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 89 289
95 % 54 89 386
90 % 54 90 396
70 % 70 159 276
50 % 71 172 276
40 % 139 243 198
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 93 284
95 % 54 95 356
90 % 54 96 363
70 % 54 96 398
50 % 73 183 243
40 % 73 183 254
30 % 73 185 268

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 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 6S47 41 Ao Ubiquitin-60S ribosomal protein L40 4932
5 6RI5 46 t Ubiquitin-60S ribosomal protein L40 4932
6 6QTZ 46 t Ubiquitin-60S ribosomal protein L40 4932
7 6QT0 41 t Ubiquitin-60S ribosomal protein L40 4932
8 6QIK 45 t Ubiquitin-60S ribosomal protein L40 4932
9 6N8M 44 z Ubiquitin-60S ribosomal protein L40 4932
10 6N8N 47 z Ubiquitin-60S ribosomal protein L40 4932
11 6N8O 49 z Ubiquitin-60S ribosomal protein L40 4932
12 6IP5 41 2g Ubiquitin-60S ribosomal protein L40 9606
13 6IP6 41 2g Ubiquitin-60S ribosomal protein L40 9606
14 6IP8 41 2g Ubiquitin-60S ribosomal protein L40 9606
15 6HD7 44 o Ubiquitin-60S ribosomal protein L40 4932
16 6EF3 24 u Ubiquitin-60S ribosomal protein L40 4932
17 6EK0 41 Lm Ubiquitin-60S ribosomal protein L40 Modified amino acid MLZ (Methyl-lysine) 9606
18 5XY3 41 m Ubiquitin, putative UNP residues 35-166 5722
19 5XXB 41 l Ribosomal protein eL40 5811
20 5UMD 42 f Ubiquitin-60S ribosomal protein L40 5833
21 5MC6 55 AO Ubiquitin-60S ribosomal protein L40 4932
22 5T62 42 z Ubiquitin-60S ribosomal protein L40 4932
23 5T6R 41 z Ubiquitin-60S ribosomal protein L40 4932
24 5T2A 43 q eL40 5661
25 5T2C 27 g Ubiquitin-60S ribosomal protein L40 9606
26 5LKS 41 Lm Ubiquitin-60S ribosomal protein L40 9606
27 5JUO 44 RA eL40 (yeast L40) 4932
28 5JUP 44 RA eL40 (yeast L40) 4932
29 5JUS 44 RA eL40 (yeast L40) 4932
30 5JUT 44 RA eL40 (yeast L40) 4932
31 5JUU 44 RA eL40 (yeast L40) 4932
32 5GAK 36 o Ubiquitin-60S ribosomal protein L40 4932
33 5APN 41 m Ubiquitin-60S ribosomal protein L40 4932
34 5APO 41 m Ubiquitin-60S ribosomal protein L40 4932
35 4UG0 41 Lm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9606
36 5AJ0 41 Am Ubiquitin-60S ribosomal protein L40 9606
37 3J92 38 m eL40 9986
38 4D67 38 m UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
39 4D5Y 38 m 60S RIBOSOMAL PROTEIN EL40 9986
40 3J7O 41 m Ribosomal protein eL40 9823
41 3J7P 42 m Ribosomal protein eL40 9823
42 3J7Q 41 m Ribosomal protein eL40 9823
43 3J7R 41 m Ribosomal protein eL40 9823
44 4UJC 44 Bm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
45 4UJD 41 Am UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
46 3J79 42 f 60S ribosomal protein eL40 5833
47 3J77 40 90 60S ribosomal protein L40 4932
48 3J78 40 90 60S ribosomal protein L40 4932
49 3J6X 42 80 60S ribosomal protein L40 4932
50 3J6Y 42 80 60S ribosomal protein L40 4932
51 4UJE 75 Cm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 9986
52 4V91 41 m EL40 RIBOSOMAL PROTEIN EL40 28985
53 4V8Y 73 Bm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 4932
54 4V8Z 73 Bm UBIQUITIN-60S RIBOSOMAL PROTEIN L40 4932
55 4V8M 78 Bs UBIQUITIN-60S RIBOSOMAL PROTEIN L40 185431
56 4V8T 39 m 60S RIBOSOMAL PROTEIN L40 4932
57 4ADX 6 5 RPL40E 145262