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 % 73 114 273
95 % 73 118 326
90 % 73 118 346
70 % 74 120 376
50 % 92 168 344
40 % 111 222 254
30 % 111 222 263
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 70 102 309
95 % 71 104 395
90 % 71 104 417
70 % 72 106 438
50 % 108 205 283
40 % 109 207 283
30 % 109 207 296
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 67 108 289
95 % 72 113 348
90 % 72 114 363
70 % 74 117 387
50 % 75 118 433
40 % 76 122 445
30 % 76 122 461
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 114 271
95 % 73 114 343
90 % 73 114 361
70 % 74 116 392
50 % 110 209 275
40 % 110 209 278
30 % 110 208 295
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 69 110 305
95 % 76 117 344
90 % 76 117 362
70 % 77 119 394
50 % 111 193 309
40 % 111 195 314
30 % 111 195 326
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 112 280
95 % 73 113 349
90 % 73 113 368
70 % 74 115 401
50 % 110 217 263
40 % 111 218 260
30 % 182 293 197
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 46 82 496
95 % 71 107 384
90 % 72 109 395
70 % 109 208 249
50 % 111 212 268
40 % 111 212 270
30 % 111 212 284
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 112 282
95 % 72 112 361
90 % 72 112 382
70 % 73 114 412
50 % 73 114 462
40 % 109 207 285
30 % 109 207 299
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 114 272
95 % 73 114 340
90 % 73 114 359
70 % 74 116 397
50 % 74 116 448
40 % 74 116 470
30 % 74 116 488
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 68 100 317
95 % 68 100 412
90 % 69 102 425
70 % 104 191 270
50 % 106 203 288
40 % 105 203 292
30 % 106 204 302
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 % 72 104 303
95 % 72 104 397
90 % 72 104 418
70 % 73 106 440
50 % 109 207 279
40 % 110 208 279
30 % 132 231 249
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 % 73 116 265
95 % 75 119 322
90 % 75 119 341
70 % 110 207 254
50 % 112 221 254
40 % 112 221 255
30 % 112 221 267
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 67 106 300
95 % 67 106 387
90 % 73 113 367
70 % 74 115 400
50 % 110 209 271
40 % 110 210 273
30 % 110 210 287
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 117 258
95 % 72 117 327
90 % 73 119 339
70 % 73 119 382
50 % 110 219 256
40 % 110 219 257
30 % 110 219 270
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 114 268
95 % 73 114 342
90 % 74 116 351
70 % 74 116 391
50 % 109 210 280
40 % 109 215 271
30 % 109 215 286
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 70 108 290
95 % 70 108 379
90 % 70 108 403
70 % 71 111 419
50 % 109 209 276
40 % 109 210 277
30 % 109 210 292
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 112 283
95 % 72 112 359
90 % 73 114 364
70 % 73 114 410
50 % 108 200 297
40 % 109 201 300
30 % 109 202 309
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 108 291
95 % 73 108 374
90 % 74 110 386
70 % 74 110 422
50 % 109 199 298
40 % 109 205 296
30 % 111 212 283
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 81 433
95 % 51 81 551
90 % 51 81 575
70 % 52 82 591
50 % 52 82 636
40 % 52 82 674
30 % 53 83 675
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 % 73 115 264
95 % 73 115 334
90 % 74 117 348
70 % 111 221 236
50 % 114 227 247
40 % 114 227 247
30 % 114 227 257
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 68 504
95 % 47 70 640
90 % 47 70 670
70 % 48 71 687
50 % 48 71 717
40 % 68 129 464
30 % 68 129 483
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 86 405
95 % 52 86 523
90 % 53 87 538
70 % 53 87 566
50 % 53 87 597
40 % 53 89 627
30 % 53 90 645
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 119 251
95 % 73 119 321
90 % 74 121 332
70 % 74 121 372
50 % 111 217 259
40 % 111 217 263
30 % 111 217 278
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 108 295
95 % 72 108 383
90 % 73 110 394
70 % 73 110 428
50 % 108 195 307
40 % 109 208 282
30 % 110 210 291
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 106 302
95 % 73 109 368
90 % 74 111 379
70 % 74 111 416
50 % 110 212 267
40 % 111 213 268
30 % 114 218 273
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 67 95 341
95 % 67 95 439
90 % 68 97 446
70 % 68 97 469
50 % 68 97 507
40 % 68 97 533
30 % 68 97 565
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 75 114 260
95 % 75 114 332
90 % 76 116 347
70 % 76 116 385
50 % 90 157 367
40 % 90 157 378
30 % 90 157 389
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 112 277
95 % 73 112 351
90 % 73 112 371
70 % 74 114 404
50 % 110 209 272
40 % 110 209 276
30 % 110 209 289
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 115 266
95 % 73 115 339
90 % 73 115 357
70 % 74 117 389
50 % 111 213 266
40 % 111 217 264
30 % 111 218 275
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 20431
95 % 4 5 19760
90 % 4 5 19354
70 % 4 5 17879
50 % 4 5 16049
40 % 4 5 14901
30 % 4 5 13540
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 113 278
95 % 72 113 357
90 % 72 113 374
70 % 73 115 407
50 % 108 205 291
40 % 109 207 291
30 % 110 208 300
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 108 297
95 % 72 108 380
90 % 72 108 406
70 % 73 110 426
50 % 108 194 311
40 % 108 194 317
30 % 108 194 331
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 118 253
95 % 73 118 323
90 % 73 118 343
70 % 74 120 378
50 % 110 212 274
40 % 111 223 251
30 % 112 225 258
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 109 292
95 % 72 113 354
90 % 72 113 376
70 % 73 115 405
50 % 73 115 460
40 % 109 202 298
30 % 109 202 311
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 73 115 262
95 % 73 115 331
90 % 73 115 354
70 % 96 172 296
50 % 110 217 258
40 % 110 217 262
30 % 110 217 277
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 108 296
95 % 72 108 386
90 % 72 108 408
70 % 73 110 430
50 % 73 110 471
40 % 74 117 460
30 % 74 117 477
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 74 112 281
95 % 74 112 352
90 % 74 112 373
70 % 109 201 261
50 % 113 218 257
40 % 113 218 259
30 % 114 219 268
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 1313
95 % 17 39 1697
90 % 30 74 863
70 % 30 77 855
50 % 30 77 877
40 % 30 77 900
30 % 30 77 938
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 30219
95 % 3 4 24334
90 % 3 4 23578
70 % 3 4 21506
50 % 23 74 1021
40 % 23 74 1045
30 % 23 74 1093
Entity #5 | Chains: X
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 20 36 1645
95 % 20 36 2055
90 % 20 36 2113
70 % 25 41 1900
50 % 27 45 1626
40 % 27 45 1660
30 % 28 47 1611
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 14035
95 % 6 7 14308
90 % 6 8 12614
70 % 6 8 11955
50 % 6 8 10936
40 % 6 8 10315
30 % 6 8 9541
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 7964
95 % 9 11 8696
90 % 9 11 8652
70 % 9 11 8405
50 % 9 11 7878
40 % 12 14 6029
30 % 12 14 5751
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 72 107 294
95 % 72 107 382
90 % 73 109 393
70 % 108 197 266
50 % 109 210 270
40 % 180 284 192
30 % 180 284 205
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 71 112 285
95 % 73 114 345
90 % 74 116 353
70 % 74 116 395
50 % 112 222 252
40 % 112 222 252
30 % 112 224 261

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 52 BO, DO 60S ribosomal protein L16-A, 60S ribosomal protein L16-B 4932
2 4U4R 52 M6, m6 60S ribosomal protein L16-A 4932
3 4U3U 52 M6, m6 60S ribosomal protein L16-A 4932
4 5TBW 17 CQ, w 60S ribosomal protein L16-A 4932
5 4U3M 52 M6, m6 60S ribosomal protein L16-A 4932
6 4U3N 52 M6, m6 60S ribosomal protein L16-A 4932
7 4U52 52 M6, m6 60S ribosomal protein L16-A 4932
8 4U4Q 52 M6, m6 60S ribosomal protein L16-A 4932
9 4U6F 52 M6, m6 60S ribosomal protein L16-A 4932
10 4U4U 52 M6, m6 60S ribosomal protein L16-A 4932
11 4U4Z 52 M6, m6 60S ribosomal protein L16-A 4932
12 4U4Y 52 M6, m6 60S ribosomal protein L16-A 4932
13 4U4N 52 M6, m6 60S ribosomal protein L16-A 4932
14 4U55 52 M6, m6 60S ribosomal protein L16-A 4932
15 5DAT 52 M6, m6 60S ribosomal protein L16-A 4932
16 5I4L 52 M6, m6 60S ribosomal protein L16-A 4932
17 4U51 52 M6, m6 60S ribosomal protein L16-A 4932
18 6HHQ 17 CQ, w 60S ribosomal protein L16-A 4932
19 5OBM 17 M6, m6 60S ribosomal protein L16-A 4932
20 4U53 52 M6, m6 60S ribosomal protein L16-A 4932
21 5ON6 17 CQ, w 60S ribosomal protein L16-A 4932
22 4U50 52 M6, m6 60S ribosomal protein L16-A 4932
23 5NDV 17 M6, m6 60S ribosomal protein L16-A 4932
24 5LYB 52 M6, m6 60S ribosomal protein L16-A 4932
25 4U56 52 M6, m6 60S ribosomal protein L16-A 4932
26 5TGA 52 M6, m6 60S ribosomal protein L16-A 4932
27 5MEI 17 CQ, w 60S ribosomal protein L16-A 4932
28 5FCJ 52 M6, m6 60S ribosomal protein L16-A 4932
29 4U4O 52 M6, m6 60S ribosomal protein L16-A 4932
30 5DGV 52 M6, m6 60S ribosomal protein L16-A 4932
31 5DGE 52 M6, m6 60S ribosomal protein L16-A 4932
32 5NDW 40 M6, m6 60S ribosomal protein L16-A 4932
33 5NDG 52 M6, m6 60S ribosomal protein L16-A 4932
34 5FCI 52 M6, m6 60S ribosomal protein L16-A 4932
35 5DC3 52 M6, m6 60S ribosomal protein L16-A 4932
36 5DGF 52 M6, m6 60S ribosomal protein L16-A 4932
37 5TGM 52 M6, m6 60S ribosomal protein L16-A 4932
38 4V7R 45 BP, DP 60S ribosomal protein L16-A 4932
39 6XIQ 14 O 60S ribosomal protein L16-A 4932
40 6XIR 14 O 60S ribosomal protein L16-A 4932
41 6Z6J 52 LO 60S ribosomal protein L16-A 4932
42 6Z6K 52 LO 60S ribosomal protein L16-A 4932
43 6WOO 17 O uL13 4932
44 6YLG 20 O 60S ribosomal protein L16-A 4932
45 6YLH 20 O 60S ribosomal protein L16-A 4932
46 6YLX 11 O 60S ribosomal protein L16-A 4932
47 6YLY 26 O 60S ribosomal protein L16-A 4932
48 6M62 21 O 60S ribosomal protein L16-A 4932
49 6TNU 54 AU 60S ribosomal protein L16-A 4932
50 6TB3 54 AU 60S ribosomal protein L16-A 4932
51 6T83 50 Oy, Qa 60S ribosomal protein L16-A 4932
52 6T7T 50 LO 60S ribosomal protein L16-A 4932
53 6T7I 50 LO 60S ribosomal protein L16-A 4932
54 6T4Q 49 LO 60S ribosomal protein L16-A 4932
55 6SV4 17 AU, XU, zU 60S ribosomal protein L16-A 4932
56 6SNT 50 u 60S ribosomal protein L16-A 4932
57 6S47 17 AQ 60S ribosomal protein L16-A 4932
58 6OIG 16 O 60S ribosomal protein L16-A 4932
59 6R84 18 Q 60S ribosomal protein L16-A 4932
60 6R86 17 Q 60S ribosomal protein L16-A 4932
61 6R87 17 Q 60S ribosomal protein L16-A 4932
62 6Q8Y 22 AU 60S ribosomal protein L16-A 4932
63 6N8J 29 O 60S ribosomal protein L16-A 4932
64 6N8K 28 O 60S ribosomal protein L16-A 4932
65 6N8L 28 O 60S ribosomal protein L16-A 4932
66 6N8M 20 b 60S ribosomal protein L16-A 4932
67 6N8N 23 b 60S ribosomal protein L16-A 4932
68 6N8O 25 b 60S ribosomal protein L16-A 4932
69 6I7O 17 AU, XU 60S ribosomal protein L16-A 4932
70 6HD7 20 Q 60S ribosomal protein L16-A 4932
71 6GQV 19 O 60S ribosomal protein L16-A 4932
72 6GQ1 19 O 60S ribosomal protein L16-A 4932
73 6GQB 19 O 60S ribosomal protein L16-A 4932
74 6FT6 15 O 60S ribosomal protein L16-A 4932
75 6CB1 15 O 60S ribosomal protein L16-A 4932
76 5Z3G 19 S 60S ribosomal protein L16-A 4932
77 6C0F 16 O 60S ribosomal protein L16-A 4932
78 6EM1 29 O 60S ribosomal protein L16-A 4932
79 6EM3 20 O 60S ribosomal protein L16-A Backbone model 4932
80 6EM4 23 O 60S ribosomal protein L16-A Backbone model 4932
81 6EM5 22 O 60S ribosomal protein L16-A Backbone model 4932
82 6ELZ 20 O 60S ribosomal protein L16-A 4932
83 5MC6 61 AU 60S ribosomal protein L16-A 4932
84 5H4P 16 O 60S ribosomal protein L16-A 4932
85 5M1J 72 K5 60S ribosomal protein L16-A 4932
86 5T62 18 b 60S ribosomal protein L16-A 4932
87 5T6R 17 b 60S ribosomal protein L16-A 4932
88 5JUO 20 T uL13 (yeast L16) 4932
89 5JUP 20 T uL13 (yeast L16) 4932
90 5JUS 20 T uL13 (yeast L16) 4932
91 5JUT 20 T uL13 (yeast L16) 4932
92 5JUU 20 T uL13 (yeast L16) 4932
93 5JCS 29 O 60S ribosomal protein L16-A 4932
94 3JCT 15 O 60S ribosomal protein L16-A 4932
95 5GAK 39 Q 60S ribosomal protein L16-A 4932
96 5FL8 15 O 60S ribosomal protein L16-A 4932
97 5APN 17 O 60S ribosomal protein L16-A 4932
98 5APO 17 O 60S ribosomal protein L16-A 4932
99 3J77 16 66 60S ribosomal protein L16 4932
100 3J78 16 66 60S ribosomal protein L16 4932
101 3J6X 18 56 60S ribosomal protein L16 4932
102 3J6Y 18 56 60S ribosomal protein L16 4932
103 4V7F 13 J 60S ribosomal protein L16 4932
104 4V8Y 49 BO 60S RIBOSOMAL PROTEIN L16-A 4932
105 4V8Z 49 BO 60S RIBOSOMAL PROTEIN L16-A 4932
106 4V6I 40 BK 60S ribosomal protein rpL16 (L13p) 4932