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 95 263
95 % 54 99 331
90 % 54 99 344
70 % 54 100 379
50 % 71 147 343
40 % 74 185 256
30 % 74 185 275
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 87 407
90 % 54 87 427
70 % 54 88 455
50 % 73 170 292
40 % 74 172 291
30 % 74 172 312
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 95 353
90 % 54 96 363
70 % 54 97 394
50 % 55 98 451
40 % 56 102 457
30 % 56 102 475
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 95 268
95 % 54 95 354
90 % 54 95 370
70 % 54 97 391
50 % 73 173 280
40 % 73 173 290
30 % 73 172 317
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 91 312
95 % 57 98 357
90 % 57 98 371
70 % 57 99 398
50 % 74 156 335
40 % 74 158 338
30 % 74 158 354
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 94 271
95 % 54 94 363
90 % 54 94 379
70 % 54 95 404
50 % 73 180 264
40 % 141 252 192
30 % 142 253 199
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 67 498
95 % 54 90 382
90 % 54 91 395
70 % 74 173 254
50 % 76 177 266
40 % 76 177 281
30 % 76 177 300
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 93 278
95 % 53 93 371
90 % 53 93 387
70 % 53 94 413
50 % 53 94 471
40 % 72 170 302
30 % 72 170 322
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 95 267
95 % 54 95 358
90 % 54 95 372
70 % 54 96 401
50 % 54 96 463
40 % 54 96 485
30 % 54 96 517
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 86 306
95 % 54 86 409
90 % 54 87 424
70 % 72 164 268
50 % 74 171 288
40 % 74 172 293
30 % 74 172 316
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 86 304
95 % 54 86 408
90 % 54 86 428
70 % 54 87 457
50 % 73 171 286
40 % 74 172 294
30 % 96 195 245
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 97 261
95 % 55 99 334
90 % 55 99 348
70 % 73 170 261
50 % 75 184 247
40 % 75 184 262
30 % 75 184 281
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 48 87 303
95 % 48 87 404
90 % 54 94 376
70 % 54 95 403
50 % 73 172 281
40 % 73 173 289
30 % 73 173 311
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 98 337
90 % 53 99 346
70 % 53 99 386
50 % 73 182 251
40 % 73 182 265
30 % 73 182 284
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 95 356
90 % 54 96 362
70 % 54 96 397
50 % 72 173 291
40 % 72 178 283
30 % 72 178 304
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 89 291
95 % 51 89 389
90 % 51 89 407
70 % 51 91 429
50 % 71 171 290
40 % 71 172 300
30 % 71 172 321
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 93 376
90 % 53 94 384
70 % 53 94 416
50 % 71 163 322
40 % 72 164 322
30 % 72 165 335
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 89 391
90 % 54 90 401
70 % 54 90 436
50 % 72 162 321
40 % 72 168 316
30 % 74 175 301
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 68 590
90 % 38 68 623
70 % 38 68 664
50 % 38 68 699
40 % 38 68 720
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 96 346
90 % 54 97 356
70 % 74 184 232
50 % 74 185 245
40 % 74 185 257
30 % 74 185 277
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 63 445
95 % 40 63 599
90 % 40 63 631
70 % 40 63 673
50 % 40 63 705
40 % 46 107 483
30 % 46 107 509
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 73 410
95 % 39 73 542
90 % 39 73 567
70 % 39 73 602
50 % 39 73 648
40 % 39 75 657
30 % 39 76 690
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 % 73 179 260
40 % 73 179 276
30 % 73 179 293
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 89 293
95 % 53 89 396
90 % 53 90 402
70 % 53 90 438
50 % 71 158 332
40 % 72 171 301
30 % 73 173 315
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 87 307
95 % 54 90 381
90 % 54 91 397
70 % 54 91 428
50 % 73 175 271
40 % 74 176 282
30 % 74 178 298
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 81 324
95 % 53 81 433
90 % 53 82 453
70 % 53 82 484
50 % 53 82 521
40 % 53 82 550
30 % 53 82 576
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 258
95 % 56 95 344
90 % 56 96 352
70 % 56 96 389
50 % 69 136 363
40 % 69 136 377
30 % 69 136 387
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 93 369
90 % 54 93 380
70 % 54 94 409
50 % 73 172 282
40 % 73 172 292
30 % 73 172 314
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 262
95 % 54 96 350
90 % 54 96 368
70 % 54 97 395
50 % 74 176 269
40 % 74 180 272
30 % 74 181 289
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 19531
95 % 4 5 17687
90 % 4 5 17356
70 % 4 5 16179
50 % 4 5 14596
40 % 4 5 13576
30 % 4 5 12361
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 94 274
95 % 53 94 367
90 % 53 94 382
70 % 53 95 412
50 % 71 168 304
40 % 72 170 310
30 % 72 170 327
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 89 295
95 % 53 89 399
90 % 53 89 421
70 % 53 90 440
50 % 71 157 334
40 % 71 157 343
30 % 71 157 357
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 99 246
95 % 54 99 330
90 % 54 99 345
70 % 54 100 381
50 % 72 174 284
40 % 73 185 255
30 % 74 187 266
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 90 288
95 % 53 94 368
90 % 53 94 385
70 % 53 95 406
50 % 53 95 468
40 % 72 165 318
30 % 72 165 334
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 96 348
90 % 54 96 359
70 % 60 134 311
50 % 73 180 255
40 % 73 180 271
30 % 73 180 291
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 300
95 % 53 89 400
90 % 53 89 417
70 % 53 90 442
50 % 53 90 489
40 % 54 97 479
30 % 54 97 504
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 92 280
95 % 54 92 372
90 % 54 92 388
70 % 72 164 267
50 % 73 176 270
40 % 73 178 279
30 % 74 179 294
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 1584
95 % 9 31 2099
90 % 10 54 1128
70 % 10 57 1083
50 % 10 57 1128
40 % 10 57 1156
30 % 10 57 1202
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 24492
95 % 3 4 20736
90 % 3 4 24045
70 % 3 4 21955
50 % 15 66 1046
40 % 15 66 1079
30 % 15 66 1126
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 1748
95 % 15 31 2270
90 % 15 31 2327
70 % 16 32 2307
50 % 18 36 1841
40 % 18 36 1879
30 % 19 38 1766
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 12605
95 % 6 7 12700
90 % 6 8 10779
70 % 6 8 10433
50 % 6 8 9641
40 % 6 8 9148
30 % 6 8 8529
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 7354
95 % 9 11 7886
90 % 9 11 7850
70 % 9 11 7676
50 % 9 11 7209
40 % 9 11 6980
30 % 9 11 6553
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 89 387
90 % 54 90 399
70 % 72 161 273
50 % 73 174 275
40 % 141 245 197
30 % 141 245 208
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 95 359
90 % 54 96 367
70 % 54 96 402
50 % 75 185 242
40 % 75 185 254
30 % 75 187 265

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 6T59 44 t3 Ribosomal protein L12 9986
4 6SGC 79 t2 Ribosomal protein L12 9986
5 6R84 26 P 60S ribosomal protein L12-A 4932
6 6R86 25 P 60S ribosomal protein L12-A 4932
7 6R87 25 P 60S ribosomal protein L12-A 4932
8 6R7Q 75 t uL11 9986
9 6R6G 79 t uL11 9986
10 6R6P 47 t Ribosomal protein L12 9986
11 6R5Q 50 t uL11 9986
12 6QKL 11 D 60S ribosomal protein L12 44689
13 6N8J 44 K 60S ribosomal protein L12 4932
14 6N8M 46 L Ribosomal protein L12 4932
15 6N8N 48 L Ribosomal protein L12 4932
16 6N8O 6 L Ribosomal protein L12 4932
17 6MTD 47 t eL11 9986
18 6MTE 47 t uL11 9986
19 6HCQ 81 u3 Ribosomal protein L12 9986
20 6HCJ 81 u3 Ribosomal protein L12 9986
21 6HCM 79 t3 Ribosomal protein L12 9986
22 6HCF 79 t3 Ribosomal protein L12 9986
23 6GZ3 84 Aq Ribosomal protein L12 9986
24 6GZ4 84 Aq ribosomal protein uL11 9986
25 6GZ5 84 Aq ribosomal protein uL11 9986
26 6FTG 44 t Ribosomal protein L12 9986
27 6FTI 44 t Ribosomal protein L12 9986
28 6FTJ 44 t Ribosomal protein L12 9986
29 6FRK 4 4 Ribosomal protein L12 9986
30 5LZS 44 t uL11 9986
31 5LZT 44 t uL11 9986
32 5LZU 44 t uL11 9986
33 5LZV 44 t uL11 9986
34 5LZW 44 t uL11 9986
35 5LZX 44 t uL11 9986
36 5LZY 44 t uL11 9986
37 5LZZ 44 t uL11 9986
38 5JUO 16 P uL11 (yeast L12) 4932
39 5JUP 16 P uL11 (yeast L12) 4932
40 5JUS 16 P uL11 (yeast L12) 4932
41 5JUT 16 P uL11 (yeast L12) 4932
42 5JUU 16 P uL11 (yeast L12) 4932
43 5JCS 21 K 60S ribosomal protein L12-A 4932
44 5FL8 11 K 60S ribosomal protein L12-A 4932
45 5AN9 4 D 60S RIBOSOMAL PROTEIN L12 44689
46 5ANB 4 D 60S RIBOSOMAL PROTEIN L12 44689
47 5ANC 4 D 60S RIBOSOMAL PROTEIN L12 44689
48 5A8L 4 G 60S RIBOSOMAL PROTEIN L12 9606
49 3JAN 46 K Ribosomal protein uL11 SEE REMARK 999 9986
50 3JAJ 46 K Ribosomal protein uL11 SEE REMARK 999 9986
51 3JAG 44 t uL11 9986
52 3JAH 44 t uL11 9986
53 3JAI 44 t uL11 9986
54 5AJ0 45 Aq 60S ribosomal protein L12 9606
55 3J92 43 t uL11 9986
56 3J7P 14 K Ribosomal protein uL11 9823
57 3J77 12 62 60S ribosomal protein L12 4932
58 3J78 12 62 60S ribosomal protein L12 4932
59 4V7F 12 I 60S ribosomal protein L12 4932
60 4V7E 65 CK 60S ribosomal protein L11 4565
61 4V6W 40 CK 60S ribosomal protein L12 7227
62 4V6X 40 CK 60S ribosomal protein L12 9606
63 4V8M 46 BM 60S RIBOSOMAL PROTEIN L12, PUTATIVE 185431
64 3J16 10 H 60S ribosomal protein L11 4932
65 4V6I 39 BJ 60S ribosomal protein rpL12 (L11p) 4932
66 4V5Z 61 Bi 60S Ribosomal protein L12 9612