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 % 62 103 266
95 % 62 107 331
90 % 62 107 350
70 % 63 109 385
50 % 81 157 344
40 % 87 198 263
30 % 87 198 279
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 93 317
95 % 62 95 401
90 % 62 95 420
70 % 63 97 439
50 % 86 183 290
40 % 87 185 293
30 % 87 185 315
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 97 293
95 % 61 102 358
90 % 61 103 370
70 % 63 106 393
50 % 64 107 447
40 % 65 111 459
30 % 65 111 477
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 103 270
95 % 62 103 350
90 % 62 103 371
70 % 63 105 398
50 % 86 185 281
40 % 86 185 298
30 % 86 184 323
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 99 321
95 % 65 106 356
90 % 65 106 375
70 % 66 108 401
50 % 87 169 327
40 % 87 171 335
30 % 87 171 354
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 102 271
95 % 62 102 359
90 % 62 102 377
70 % 63 104 405
50 % 86 193 272
40 % 87 195 274
30 % 155 266 205
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 75 490
95 % 62 98 387
90 % 63 100 394
70 % 87 186 259
50 % 89 190 271
40 % 89 190 284
30 % 89 190 300
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 101 282
95 % 61 101 373
90 % 61 101 393
70 % 62 103 414
50 % 62 103 465
40 % 85 183 305
30 % 85 183 328
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 103 269
95 % 62 103 357
90 % 62 103 376
70 % 63 105 404
50 % 63 105 459
40 % 63 105 487
30 % 63 105 505
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 94 308
95 % 62 94 407
90 % 63 96 411
70 % 85 169 282
50 % 87 181 299
40 % 86 181 308
30 % 87 182 329
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 % 62 94 310
95 % 62 94 405
90 % 62 94 423
70 % 63 96 443
50 % 86 184 283
40 % 87 185 294
30 % 109 208 258
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 % 62 105 262
95 % 64 108 330
90 % 64 108 348
70 % 86 183 266
50 % 88 197 254
40 % 88 197 268
30 % 88 197 283
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 307
95 % 56 95 403
90 % 62 102 380
70 % 63 104 407
50 % 63 105 458
40 % 63 106 484
30 % 63 106 502
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 106 257
95 % 61 106 334
90 % 62 108 342
70 % 62 108 389
50 % 86 195 259
40 % 86 195 272
30 % 86 195 288
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 103 268
95 % 62 103 355
90 % 63 105 363
70 % 63 105 403
50 % 85 186 287
40 % 85 191 289
30 % 85 191 311
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 59 97 297
95 % 59 97 391
90 % 59 97 408
70 % 60 100 421
50 % 85 185 285
40 % 85 186 296
30 % 85 186 320
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 101 283
95 % 61 101 377
90 % 62 103 383
70 % 62 103 416
50 % 84 176 318
40 % 85 177 324
30 % 85 178 337
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 97 294
95 % 62 97 390
90 % 63 99 400
70 % 63 99 428
50 % 85 175 316
40 % 85 181 317
30 % 87 188 309
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 42 72 464
95 % 42 72 606
90 % 42 72 635
70 % 43 73 657
50 % 43 73 685
40 % 43 73 723
30 % 44 74 722
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 % 62 104 265
95 % 62 104 348
90 % 63 106 353
70 % 87 197 240
50 % 87 198 252
40 % 87 198 262
30 % 87 198 277
Entity #31 | Chains: j
60S ribosomal protein L24-A protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 41 64 483
95 % 43 66 629
90 % 43 66 660
70 % 44 67 678
50 % 44 67 716
40 % 53 114 491
30 % 53 114 512
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 43 77 434
95 % 43 77 560
90 % 44 78 581
70 % 44 78 601
50 % 44 78 635
40 % 44 80 660
30 % 44 81 671
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 108 250
95 % 62 108 322
90 % 63 110 334
70 % 63 110 382
50 % 87 193 265
40 % 87 193 279
30 % 87 193 293
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 97 304
95 % 61 97 396
90 % 62 99 404
70 % 62 99 436
50 % 84 171 325
40 % 85 184 299
30 % 86 186 316
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 95 309
95 % 62 98 383
90 % 63 100 391
70 % 63 100 420
50 % 86 188 275
40 % 87 189 288
30 % 87 191 299
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 89 330
95 % 61 89 434
90 % 62 91 444
70 % 62 91 472
50 % 62 91 508
40 % 62 91 548
30 % 62 91 576
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 64 103 263
95 % 64 103 346
90 % 65 105 352
70 % 65 105 395
50 % 79 146 361
40 % 79 146 375
30 % 79 146 391
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 101 275
95 % 62 101 369
90 % 62 101 388
70 % 63 103 410
50 % 86 185 282
40 % 86 185 295
30 % 86 185 319
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 104 264
95 % 62 104 347
90 % 62 104 368
70 % 63 106 396
50 % 87 189 274
40 % 87 193 280
30 % 87 194 290
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 20761
95 % 4 5 18730
90 % 4 5 18387
70 % 4 5 17076
50 % 4 5 15375
40 % 4 5 14268
30 % 4 5 12984
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 102 274
95 % 61 102 366
90 % 61 102 384
70 % 62 104 411
50 % 84 181 307
40 % 85 183 313
30 % 85 183 334
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 97 300
95 % 61 97 393
90 % 61 97 410
70 % 62 99 430
50 % 84 170 326
40 % 84 170 338
30 % 84 170 358
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 107 253
95 % 62 107 328
90 % 62 107 346
70 % 63 109 384
50 % 86 188 280
40 % 87 199 259
30 % 88 201 270
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 98 299
95 % 61 102 370
90 % 61 102 389
70 % 62 104 413
50 % 62 104 463
40 % 85 178 320
30 % 85 188 312
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 104 261
95 % 62 104 345
90 % 62 104 366
70 % 72 148 309
50 % 86 193 266
40 % 86 193 282
30 % 86 193 295
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 97 305
95 % 61 97 399
90 % 61 97 416
70 % 62 99 438
50 % 62 99 486
40 % 63 106 474
30 % 63 106 495
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 63 101 277
95 % 63 101 368
90 % 63 101 386
70 % 85 177 275
50 % 86 189 273
40 % 86 191 283
30 % 87 192 297
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 35 1346
95 % 14 36 1736
90 % 18 62 992
70 % 18 65 967
50 % 18 65 999
40 % 18 65 1030
30 % 18 65 1082
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 29338
95 % 3 4 24110
90 % 3 4 19923
70 % 3 4 20922
50 % 15 66 1128
40 % 15 66 1169
30 % 15 66 1215
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 1880
95 % 15 31 2400
90 % 15 31 2459
70 % 16 32 2421
50 % 18 36 1956
40 % 18 36 2000
30 % 19 38 1896
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 13966
95 % 6 7 13463
90 % 6 8 11535
70 % 6 8 11037
50 % 6 8 10207
40 % 6 8 9698
30 % 6 8 9016
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 7670
95 % 9 11 8421
90 % 9 11 8372
70 % 9 11 8189
50 % 9 11 7699
40 % 9 11 7409
30 % 9 11 6981
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 97 295
95 % 62 97 388
90 % 63 99 396
70 % 85 174 280
50 % 86 187 277
40 % 154 258 200
30 % 154 258 212
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 60 101 289
95 % 62 103 354
90 % 63 105 361
70 % 63 105 400
50 % 88 198 251
40 % 88 198 261
30 % 88 200 271

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