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 4V88 67 Bd, Dd 60S ribosomal protein L31-A 4932
2 4U4R 67 O1, o1 60S ribosomal protein L31-A 4932
3 4U3U 67 O1, o1 60S ribosomal protein L31-A 4932
4 5TBW 32 AE, DF 60S ribosomal protein L31-A 4932
5 4U3M 67 O1, o1 60S ribosomal protein L31-A 4932
6 4U3N 67 O1, o1 60S ribosomal protein L31-A 4932
7 4U52 67 O1, o1 60S ribosomal protein L31-A 4932
8 4U4Q 67 O1, o1 60S ribosomal protein L31-A 4932
9 4U6F 67 O1, o1 60S ribosomal protein L31-A 4932
10 4U4U 67 O1, o1 60S ribosomal protein L31-A 4932
11 4U4Z 67 O1, o1 60S ribosomal protein L31-A 4932
12 4U4Y 67 O1, o1 60S ribosomal protein L31-A 4932
13 4U4N 67 O1, o1 60S ribosomal protein L31-A 4932
14 4U55 67 O1, o1 60S ribosomal protein L31-A 4932
15 5DAT 67 O1, o1 60S ribosomal protein L31-A 4932
16 5I4L 67 O1, o1 60S ribosomal protein L31-A 4932
17 4U51 67 O1, o1 60S ribosomal protein L31-A 4932
18 6HHQ 32 AE, DF 60S ribosomal protein L31-A 4932
19 5OBM 32 O1, o1 60S ribosomal protein L31-A 4932
20 4U53 67 O1, o1 60S ribosomal protein L31-A 4932
21 5ON6 33 AE, DF 60S ribosomal protein L31-A 4932
22 4U50 67 O1, o1 60S ribosomal protein L31-A 4932
23 5NDV 32 O1, o1 60S ribosomal protein L31-A 4932
24 5LYB 67 O1, o1 60S ribosomal protein L31-A 4932
25 4U56 67 O1, o1 60S ribosomal protein L31-A 4932
26 5TGA 67 O1, o1 60S ribosomal protein L31-A 4932
27 5MEI 33 AE, DF 60S ribosomal protein L31-A 4932
28 5FCJ 67 O1, o1 60S ribosomal protein L31-A 4932
29 4U4O 67 O1, o1 60S ribosomal protein L31-A 4932
30 5DGV 67 O1, o1 60S ribosomal protein L31-A 4932
31 5DGE 67 O1, o1 60S ribosomal protein L31-A 4932
32 5NDW 55 O1, o1 60S ribosomal protein L31-A 4932
33 5NDG 67 O1, o1 60S ribosomal protein L31-A 4932
34 5FCI 67 O1, o1 60S ribosomal protein L31-A 4932
35 5DC3 67 O1, o1 60S ribosomal protein L31-A 4932
36 5DGF 67 O1, o1 60S ribosomal protein L31-A 4932
37 5TGM 67 O1, o1 60S ribosomal protein L31-A 4932
38 4V7R 56 Ba, Da 60S ribosomal protein L31-A 4932
39 6S47 32 Af 60S ribosomal protein L31-A 4932
40 6RZZ 29 d 60S ribosomal protein L31-A 4932
41 6S05 29 d 60S ribosomal protein L31-A 4932
42 6RI5 29 d 60S ribosomal protein L31-A 4932
43 6R84 43 f 60S ribosomal protein L31-A 4932
44 6R86 41 f 60S ribosomal protein L31-A 4932
45 6R87 42 f 60S ribosomal protein L31-A 4932
46 6QTZ 29 d 60S ribosomal protein L31-A 4932
47 6QT0 30 d 60S ribosomal protein L31-A 4932
48 6QIK 29 d 60S ribosomal protein L31-A 4932
49 6Q8Y 40 BC 60S ribosomal protein L31-A 4932
50 6N8J 9 d 60S ribosomal protein L31-A 4932
51 6N8K 9 d 60S ribosomal protein L31-A 4932
52 6N8L 9 d 60S ribosomal protein L31-A 4932
53 6N8M 35 q 60S ribosomal protein L31-A 4932
54 6N8N 38 q 60S ribosomal protein L31-A 4932
55 6N8O 40 q 60S ribosomal protein L31-A 4932
56 6I7O 66 BC, YC 60S ribosomal protein L31-A 4932
57 6HD7 35 f 60S ribosomal protein L31-A 4932
58 6GQV 34 d 60S ribosomal protein L31-A 4932
59 6GQ1 34 d 60S ribosomal protein L31-A 4932
60 6GQB 34 d 60S ribosomal protein L31-A 4932
61 6FT6 30 d 60S ribosomal protein L31-A 4932
62 6EM5 13 d 60S ribosomal protein L31-A Backbone model 4932
63 6ELZ 13 d 60S ribosomal protein L31-A 4932
64 5MC6 69 BC 60S ribosomal protein L31-A 4932
65 5H4P 31 d 60S ribosomal protein L31-A 4932
66 5M1J 46 d5 60S ribosomal protein L31-A 4932
67 5T62 33 q 60S ribosomal protein L31-A 4932
68 5T6R 32 q 60S ribosomal protein L31-A 4932
69 5JUO 35 IA eL31 (yeast L31) 4932
70 5JUP 35 IA eL31 (yeast L31) 4932
71 5JUS 35 IA eL31 (yeast L31) 4932
72 5JUT 35 IA eL31 (yeast L31) 4932
73 5JUU 35 IA eL31 (yeast L31) 4932
74 5JCS 4 d 60S ribosomal protein L31-A 4932
75 3JCT 30 d 60S ribosomal protein L31-A 4932
76 5GAK 18 f 60S ribosomal protein L31-A 4932
77 5FL8 28 d 60S ribosomal protein L31-A 4932
78 5APN 32 d 60S ribosomal protein L31-A 4932
79 5APO 32 d 60S ribosomal protein L31-A 4932
80 3J77 31 81 60S ribosomal protein L31 4932
81 3J78 31 81 60S ribosomal protein L31 4932
82 3J6X 33 71 60S ribosomal protein L31 4932
83 3J6Y 33 71 60S ribosomal protein L31 4932
84 4V91 32 d EL31 RIBOSOMAL PROTEIN EL31 28985
85 4V7F 32 c 60S ribosomal protein L31 4932
86 4V8Y 64 Bd 60S RIBOSOMAL PROTEIN L31-A 4932
87 4V8Z 64 Bd 60S RIBOSOMAL PROTEIN L31-A 4932
88 4V8T 30 d 60S RIBOSOMAL PROTEIN L31-A 4932
89 4V6I 58 Bg 60S ribosomal protein rpL31 (L31e) 4932
90 2WW9 13 M 60S RIBOSOMAL PROTEIN L31-A 4932
91 2WWA 13 M 60S RIBOSOMAL PROTEIN L31-A 4932
92 2WWB 13 M 60S RIBOSOMAL PROTEIN L31-A 4565
93 4V4B 43 BW 60S ribosomal protein L31 4932