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 % 75 116 271
95 % 75 120 324
90 % 75 120 343
70 % 76 122 375
50 % 96 172 339
40 % 114 225 261
30 % 114 225 271
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 104 309
95 % 73 106 393
90 % 73 106 416
70 % 74 108 441
50 % 111 208 282
40 % 113 211 285
30 % 113 211 299
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 69 110 288
95 % 74 115 355
90 % 74 116 367
70 % 76 119 390
50 % 77 120 429
40 % 78 124 447
30 % 78 124 464
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 116 273
95 % 75 116 351
90 % 75 116 369
70 % 76 118 400
50 % 114 213 274
40 % 114 213 281
30 % 115 213 296
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 71 112 305
95 % 78 119 347
90 % 78 119 368
70 % 79 121 397
50 % 114 196 307
40 % 115 199 311
30 % 115 199 328
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 114 277
95 % 75 115 354
90 % 75 115 373
70 % 76 117 405
50 % 76 121 435
40 % 115 223 265
30 % 187 298 198
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 48 84 494
95 % 73 109 381
90 % 74 111 394
70 % 112 211 248
50 % 116 217 263
40 % 116 217 274
30 % 116 217 286
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 114 283
95 % 74 114 364
90 % 74 114 386
70 % 75 116 415
50 % 75 116 457
40 % 113 211 287
30 % 113 211 302
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 116 272
95 % 75 116 346
90 % 75 116 366
70 % 76 118 399
50 % 76 118 448
40 % 76 118 472
30 % 76 118 491
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 68 100 323
95 % 68 100 418
90 % 69 102 434
70 % 105 192 275
50 % 109 206 284
40 % 109 207 292
30 % 109 207 306
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 % 74 106 304
95 % 74 106 394
90 % 74 106 417
70 % 75 108 442
50 % 115 213 272
40 % 115 213 279
30 % 137 236 259
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 % 75 118 265
95 % 77 121 323
90 % 77 121 342
70 % 113 210 249
50 % 117 226 254
40 % 187 299 188
30 % 187 299 199
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 69 108 300
95 % 69 108 388
90 % 75 115 375
70 % 76 117 402
50 % 113 212 276
40 % 113 213 280
30 % 113 213 295
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 119 256
95 % 74 119 329
90 % 75 121 339
70 % 75 121 381
50 % 114 223 257
40 % 115 227 258
30 % 185 301 195
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 116 269
95 % 75 116 344
90 % 76 118 354
70 % 76 118 394
50 % 112 213 281
40 % 113 219 275
30 % 113 219 288
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 110 289
95 % 72 110 374
90 % 72 110 401
70 % 73 113 420
50 % 112 212 277
40 % 112 213 284
30 % 112 213 298
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 114 284
95 % 74 114 369
90 % 75 116 379
70 % 75 116 417
50 % 111 203 296
40 % 112 204 302
30 % 114 207 307
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 110 291
95 % 75 110 375
90 % 76 112 390
70 % 76 112 423
50 % 112 202 297
40 % 112 205 303
30 % 116 217 287
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 83 435
95 % 53 83 557
90 % 53 83 582
70 % 54 84 595
50 % 54 84 635
40 % 54 84 679
30 % 55 85 675
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 % 75 117 267
95 % 75 117 336
90 % 76 119 351
70 % 115 225 240
50 % 120 233 244
40 % 120 233 250
30 % 123 240 252
Entity #31 | Chains: j
60S ribosomal protein L24-A protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 45 68 515
95 % 47 70 649
90 % 47 70 683
70 % 48 71 699
50 % 48 71 730
40 % 68 129 474
30 % 68 129 492
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 88 410
95 % 54 88 516
90 % 55 89 537
70 % 55 89 565
50 % 55 89 596
40 % 55 91 615
30 % 55 92 643
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 121 249
95 % 75 121 322
90 % 76 123 338
70 % 76 123 371
50 % 114 220 261
40 % 114 220 269
30 % 114 220 280
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 110 297
95 % 74 110 382
90 % 75 112 395
70 % 75 112 427
50 % 111 198 306
40 % 113 212 286
30 % 115 215 292
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 108 301
95 % 75 111 371
90 % 76 113 385
70 % 76 113 419
50 % 114 216 264
40 % 116 218 272
30 % 119 223 273
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 67 95 348
95 % 67 95 446
90 % 68 97 458
70 % 68 97 474
50 % 68 97 518
40 % 68 97 548
30 % 68 97 579
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 77 116 264
95 % 77 116 343
90 % 78 118 353
70 % 78 118 392
50 % 94 164 351
40 % 94 164 365
30 % 94 164 375
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 114 279
95 % 75 114 360
90 % 75 114 380
70 % 76 116 407
50 % 113 212 275
40 % 113 212 282
30 % 113 212 297
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 117 260
95 % 75 117 335
90 % 75 117 359
70 % 76 119 389
50 % 113 215 266
40 % 115 221 266
30 % 115 222 276
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 21682
95 % 4 5 18646
90 % 4 5 18274
70 % 4 5 17702
50 % 4 5 15172
40 % 4 5 14070
30 % 4 5 13377
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 115 278
95 % 74 115 361
90 % 74 115 381
70 % 75 117 409
50 % 111 208 287
40 % 113 211 291
30 % 114 213 303
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 110 295
95 % 74 110 384
90 % 74 110 406
70 % 75 112 430
50 % 111 197 308
40 % 113 200 313
30 % 114 205 308
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 120 251
95 % 75 120 326
90 % 75 120 348
70 % 76 122 376
50 % 114 216 273
40 % 115 227 257
30 % 117 230 261
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 111 290
95 % 74 115 362
90 % 74 115 382
70 % 75 117 412
50 % 75 117 454
40 % 112 205 295
30 % 112 215 291
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 117 262
95 % 75 117 339
90 % 75 117 362
70 % 76 122 377
50 % 113 220 259
40 % 113 220 267
30 % 113 220 278
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 110 293
95 % 74 110 379
90 % 74 110 408
70 % 75 112 432
50 % 75 112 465
40 % 76 119 466
30 % 76 119 483
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 112 285
95 % 74 112 370
90 % 74 112 391
70 % 110 202 261
50 % 115 220 260
40 % 115 220 268
30 % 115 220 279
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 16 38 1345
95 % 17 39 1713
90 % 30 74 881
70 % 30 77 871
50 % 30 77 887
40 % 31 78 907
30 % 31 78 944
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 30583
95 % 3 4 24487
90 % 3 4 23743
70 % 3 4 21656
50 % 23 74 1035
40 % 23 74 1070
30 % 23 74 1123
Entity #5 | Chains: X
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 22 38 1555
95 % 22 38 2001
90 % 22 38 2058
70 % 27 43 1863
50 % 29 47 1615
40 % 29 47 1644
30 % 30 49 1590
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 14171
95 % 6 7 14349
90 % 6 8 11722
70 % 6 8 11191
50 % 6 8 11084
40 % 6 8 10440
30 % 6 8 9543
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 8295
95 % 9 11 8885
90 % 9 11 8829
70 % 9 11 8559
50 % 9 11 8020
40 % 12 14 6170
30 % 12 14 5868
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 109 292
95 % 74 109 385
90 % 75 111 397
70 % 111 200 264
50 % 113 214 268
40 % 185 289 196
30 % 185 289 206
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 114 287
95 % 75 116 348
90 % 76 118 357
70 % 76 118 398
50 % 117 227 250
40 % 117 227 256
30 % 117 229 262

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 6ZMO 47 Lt 60S ribosomal protein L12 9606
4 6ZME 47 Lt 60S ribosomal protein L12 9606
5 6ZMI 47 Lt 60S ribosomal protein L12 9606
6 6ZM7 47 Lt 60S ribosomal protein L12 9606
7 6XIQ 32 P2 RPL12A isoform 1 4932
8 6YLG 48 q 60S ribosomal protein L12-A 4932
9 6YLH 48 q 60S ribosomal protein L12-A 4932
10 6T59 44 t3 Ribosomal protein L12 9986
11 6SGC 79 t2 Ribosomal protein L12 9986
12 6OIG 12 s 60S ribosomal protein L12-A 4932
13 6R84 26 P 60S ribosomal protein L12-A 4932
14 6R86 25 P 60S ribosomal protein L12-A 4932
15 6R87 25 P 60S ribosomal protein L12-A 4932
16 6R7Q 75 t uL11 9986
17 6R6G 79 t uL11 9986
18 6R6P 47 t Ribosomal protein L12 9986
19 6R5Q 50 t uL11 9986
20 6QKL 11 D 60S ribosomal protein L12 44689
21 6N8J 44 K 60S ribosomal protein L12 4932
22 6N8M 46 L Ribosomal protein L12 4932
23 6N8N 48 L Ribosomal protein L12 4932
24 6N8O 6 L Ribosomal protein L12 4932
25 6MTD 47 t eL11 9986
26 6MTE 47 t uL11 9986
27 6HCQ 81 u3 Ribosomal protein L12 9986
28 6HCJ 81 u3 Ribosomal protein L12 9986
29 6HCM 79 t3 Ribosomal protein L12 9986
30 6HCF 79 t3 Ribosomal protein L12 9986
31 6GZ3 84 Aq Ribosomal protein L12 9986
32 6GZ4 84 Aq ribosomal protein uL11 9986
33 6GZ5 84 Aq ribosomal protein uL11 9986
34 6FTG 44 t Ribosomal protein L12 9986
35 6FTI 44 t Ribosomal protein L12 9986
36 6FTJ 44 t Ribosomal protein L12 9986
37 6FRK 4 4 Ribosomal protein L12 9986
38 5LZS 44 t uL11 9986
39 5LZT 44 t uL11 9986
40 5LZU 44 t uL11 9986
41 5LZV 44 t uL11 9986
42 5LZW 44 t uL11 9986
43 5LZX 44 t uL11 9986
44 5LZY 44 t uL11 9986
45 5LZZ 44 t uL11 9986
46 5JUO 16 P uL11 (yeast L12) 4932
47 5JUP 16 P uL11 (yeast L12) 4932
48 5JUS 16 P uL11 (yeast L12) 4932
49 5JUT 16 P uL11 (yeast L12) 4932
50 5JUU 16 P uL11 (yeast L12) 4932
51 5JCS 21 K 60S ribosomal protein L12-A 4932
52 5FL8 11 K 60S ribosomal protein L12-A 4932
53 5AN9 4 D 60S RIBOSOMAL PROTEIN L12 44689
54 5ANB 4 D 60S RIBOSOMAL PROTEIN L12 44689
55 5ANC 4 D 60S RIBOSOMAL PROTEIN L12 44689
56 5A8L 4 G 60S RIBOSOMAL PROTEIN L12 9606
57 3JAN 46 K Ribosomal protein uL11 SEE REMARK 999 9986
58 3JAJ 46 K Ribosomal protein uL11 SEE REMARK 999 9986
59 3JAG 44 t uL11 9986
60 3JAH 44 t uL11 9986
61 3JAI 44 t uL11 9986
62 5AJ0 45 Aq 60S ribosomal protein L12 9606
63 3J92 43 t uL11 9986
64 3J7P 14 K Ribosomal protein uL11 9823
65 3J77 12 62 60S ribosomal protein L12 4932
66 3J78 12 62 60S ribosomal protein L12 4932
67 4V7F 12 I 60S ribosomal protein L12 4932
68 4V7E 65 CK 60S ribosomal protein L11 4565
69 4V6W 40 CK 60S ribosomal protein L12 7227
70 4V6X 40 CK 60S ribosomal protein L12 9606
71 4V8M 46 BM 60S RIBOSOMAL PROTEIN L12, PUTATIVE 185431
72 3J16 10 H 60S ribosomal protein L11 4932
73 4V6I 39 BJ 60S ribosomal protein rpL12 (L11p) 4932
74 4V5Z 61 Bi 60S Ribosomal protein L12 9612