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 % 52 93 256
95 % 52 97 326
90 % 52 97 339
70 % 52 98 375
50 % 65 141 338
40 % 66 177 255
30 % 66 177 274
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 83 299
95 % 52 85 390
90 % 52 85 409
70 % 52 86 436
50 % 65 162 289
40 % 66 164 293
30 % 66 164 311
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 257
95 % 52 93 352
90 % 52 94 357
70 % 52 95 388
50 % 53 96 442
40 % 54 100 448
30 % 54 100 470
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 252
95 % 52 93 343
90 % 52 93 359
70 % 52 95 384
50 % 65 165 275
40 % 65 165 292
30 % 65 164 318
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 48 89 304
95 % 55 96 345
90 % 55 96 361
70 % 55 97 389
50 % 68 150 328
40 % 68 152 342
30 % 68 152 355
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 92 258
95 % 52 92 354
90 % 52 92 368
70 % 52 93 402
50 % 65 172 265
40 % 66 174 268
30 % 134 245 202
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 29 65 482
95 % 52 88 375
90 % 52 89 384
70 % 66 165 248
50 % 68 169 263
40 % 68 169 280
30 % 68 169 302
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 91 266
95 % 51 91 364
90 % 51 91 379
70 % 51 92 415
50 % 51 92 464
40 % 64 162 308
30 % 64 162 327
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 255
95 % 52 93 348
90 % 52 93 363
70 % 52 94 392
50 % 52 94 452
40 % 52 94 480
30 % 52 94 508
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 84 293
95 % 52 84 392
90 % 52 85 408
70 % 64 151 272
50 % 66 163 282
40 % 65 163 299
30 % 66 164 315
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 % 52 84 296
95 % 52 84 395
90 % 52 84 413
70 % 52 85 442
50 % 65 163 281
40 % 66 164 295
30 % 88 187 253
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 % 52 95 244
95 % 53 97 328
90 % 53 97 341
70 % 65 162 253
50 % 67 176 245
40 % 67 176 262
30 % 67 176 281
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 46 85 291
95 % 46 85 391
90 % 52 92 367
70 % 52 93 398
50 % 65 164 277
40 % 65 165 290
30 % 65 165 309
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 96 237
95 % 51 96 331
90 % 51 97 338
70 % 51 97 379
50 % 65 174 249
40 % 65 174 267
30 % 65 174 285
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 253
95 % 52 93 347
90 % 52 94 353
70 % 52 94 391
50 % 64 165 287
40 % 64 170 288
30 % 64 170 305
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 50 88 276
95 % 50 88 374
90 % 50 88 392
70 % 50 90 419
50 % 64 164 280
40 % 64 165 298
30 % 64 165 317
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 91 267
95 % 51 91 365
90 % 51 92 376
70 % 51 92 418
50 % 63 155 325
40 % 64 156 328
30 % 64 157 342
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 87 283
95 % 52 87 379
90 % 52 88 393
70 % 52 88 427
50 % 64 154 322
40 % 64 160 321
30 % 66 167 306
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 37 67 417
95 % 37 67 558
90 % 37 67 588
70 % 37 67 628
50 % 37 67 665
40 % 37 67 693
30 % 38 68 697
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 % 52 94 245
95 % 52 94 336
90 % 52 95 347
70 % 66 176 235
50 % 66 177 240
40 % 66 177 256
30 % 66 177 275
Entity #31 | Chains: j
60S ribosomal protein L24-A protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 62 419
95 % 39 62 571
90 % 39 62 596
70 % 39 62 635
50 % 39 62 678
40 % 39 100 490
30 % 39 100 514
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 38 72 392
95 % 38 72 518
90 % 38 72 541
70 % 38 72 572
50 % 38 72 605
40 % 38 74 623
30 % 38 75 650
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 98 232
95 % 52 98 322
90 % 52 99 330
70 % 52 99 372
50 % 65 171 259
40 % 65 171 276
30 % 65 171 298
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 87 289
95 % 51 87 385
90 % 51 88 397
70 % 51 88 434
50 % 63 150 329
40 % 64 163 302
30 % 65 165 313
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 85 295
95 % 52 88 373
90 % 52 89 380
70 % 52 89 425
50 % 65 167 269
40 % 66 168 286
30 % 66 170 300
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 79 308
95 % 51 79 413
90 % 51 80 435
70 % 51 80 466
50 % 51 80 499
40 % 51 80 531
30 % 51 80 556
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 93 248
95 % 54 93 341
90 % 54 94 348
70 % 54 94 387
50 % 67 134 351
40 % 67 134 370
30 % 67 134 381
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 91 262
95 % 52 91 360
90 % 52 91 371
70 % 52 92 408
50 % 65 164 278
40 % 65 164 297
30 % 65 164 316
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 94 246
95 % 52 94 337
90 % 52 94 351
70 % 52 95 386
50 % 66 168 266
40 % 66 172 270
30 % 66 173 289
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 17191
95 % 4 5 16914
90 % 4 5 16653
70 % 4 5 14908
50 % 4 5 14049
40 % 4 5 13052
30 % 4 5 11413
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 92 261
95 % 51 92 358
90 % 51 92 373
70 % 51 93 406
50 % 63 160 306
40 % 64 162 316
30 % 64 162 334
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 87 288
95 % 51 87 388
90 % 51 87 407
70 % 51 88 432
50 % 63 149 332
40 % 63 149 349
30 % 63 149 362
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 97 235
95 % 52 97 327
90 % 52 97 340
70 % 52 98 373
50 % 64 166 285
40 % 65 177 252
30 % 66 179 269
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 88 281
95 % 51 92 361
90 % 51 92 372
70 % 51 93 409
50 % 51 93 461
40 % 64 157 323
30 % 64 167 307
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 94 247
95 % 52 94 335
90 % 52 94 350
70 % 52 126 318
50 % 65 172 255
40 % 65 172 273
30 % 65 172 293
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 51 87 290
95 % 51 87 389
90 % 51 87 405
70 % 51 88 433
50 % 51 88 477
40 % 52 95 468
30 % 52 95 494
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 90 265
95 % 52 90 363
90 % 52 90 377
70 % 64 156 267
50 % 65 168 268
40 % 65 170 278
30 % 66 171 296
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 8 30 1588
95 % 8 30 2078
90 % 9 53 1096
70 % 9 56 1050
50 % 9 56 1089
40 % 9 56 1130
30 % 9 56 1174
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 22190
95 % 3 4 23869
90 % 3 4 19503
70 % 3 4 21208
50 % 12 63 1052
40 % 12 63 1092
30 % 12 63 1130
Entity #5 | Chains: X
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 14 30 1696
95 % 14 30 2250
90 % 14 30 2303
70 % 15 31 2290
50 % 17 35 1785
40 % 17 35 1844
30 % 18 37 1725
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 12517
95 % 6 7 12428
90 % 6 8 11143
70 % 6 8 10484
50 % 6 8 9646
40 % 6 8 9141
30 % 6 8 8469
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 6930
95 % 9 11 7546
90 % 9 11 7538
70 % 9 11 7389
50 % 9 11 6959
40 % 9 11 6734
30 % 9 11 6319
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 87 286
95 % 52 87 376
90 % 52 88 390
70 % 64 153 269
50 % 65 166 271
40 % 133 237 197
30 % 133 237 205
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 50 91 270
95 % 52 93 350
90 % 52 94 356
70 % 52 94 396
50 % 67 177 238
40 % 67 177 251
30 % 67 179 268

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 64 Ba, Da 60S ribosomal protein L28 4932
2 4U4R 64 N8, n8 60S ribosomal protein L28 4932
3 4U3U 64 N8, n8 60S ribosomal protein L28 4932
4 5TBW 29 AB, DC 60S ribosomal protein L28 4932
5 4U3M 64 N8, n8 60S ribosomal protein L28 4932
6 4U3N 64 N8, n8 60S ribosomal protein L28 4932
7 4U52 64 N8, n8 60S ribosomal protein L28 4932
8 4U4Q 64 N8, n8 60S ribosomal protein L28 4932
9 4U6F 64 N8, n8 60S ribosomal protein L28 4932
10 4U4U 64 N8, n8 60S ribosomal protein L28 4932
11 4U4Z 64 N8, n8 60S ribosomal protein L28 4932
12 4U4Y 64 N8, n8 60S ribosomal protein L28 4932
13 4U4N 64 N8, n8 60S ribosomal protein L28 4932
14 4U55 64 N8, n8 60S ribosomal protein L28 4932
15 5DAT 64 N8, n8 60S ribosomal protein L28 4932
16 5I4L 64 N8, n8 60S ribosomal protein L28 4932
17 4U51 64 N8, n8 60S ribosomal protein L28 4932
18 6HHQ 29 AB, DC 60S ribosomal protein L28 4932
19 5OBM 29 N8, n8 60S ribosomal protein L28 4932
20 4U53 64 N8, n8 60S ribosomal protein L28 4932
21 5ON6 30 AB, DC 60S ribosomal protein L28 4932
22 4U50 64 N8, n8 60S ribosomal protein L28 4932
23 5NDV 29 N8, n8 60S ribosomal protein L28 4932
24 5LYB 64 N8, n8 60S ribosomal protein L28 4932
25 4U56 64 N8, n8 60S ribosomal protein L28 4932
26 5TGA 64 N8, n8 60S ribosomal protein L28 4932
27 5MEI 30 AB, DC 60S ribosomal protein L28 4932
28 5FCJ 64 N8, n8 60S ribosomal protein L28 4932
29 4U4O 64 N8, n8 60S ribosomal protein L28 4932
30 5DGV 64 N8, n8 60S ribosomal protein L28 4932
31 5DGE 64 N8, n8 60S ribosomal protein L28 4932
32 5NDW 52 N8, n8 60S ribosomal protein L28 4932
33 5NDG 64 N8, n8 60S ribosomal protein L28 4932
34 5FCI 64 N8, n8 60S ribosomal protein L28 4932
35 5DC3 64 N8, n8 60S ribosomal protein L28 4932
36 5DGF 64 N8, n8 60S ribosomal protein L28 4932
37 5TGM 64 N8, n8 60S ribosomal protein L28 4932
38 6RZZ 13 N 60S ribosomal protein L28 4932
39 6S05 13 N 60S ribosomal protein L28 4932
40 6RI5 13 N 60S ribosomal protein L28 MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPGYFGKVGMRY FHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIPN VPVIVKARFVSKLAEEKIRAAGGVVELIA 4932
41 6R84 37 c 60S ribosomal protein L28 4932
42 6R87 36 c 60S ribosomal protein L28 4932
43 6QTZ 13 N 60S ribosomal protein L28 4932
44 6QT0 14 N 60S ribosomal protein L28 4932
45 6QIK 13 N 60S ribosomal protein L28 4932
46 6Q8Y 19 AR 60S ribosomal protein L28 4932
47 6N8J 4 a 60S ribosomal protein L28 4932
48 6N8K 4 a 60S ribosomal protein L28 4932
49 6N8L 4 a 60S ribosomal protein L28 4932
50 6N8M 32 n 60S ribosomal protein L28 4932
51 6N8N 35 n 60S ribosomal protein L28 4932
52 6N8O 37 n 60S ribosomal protein L28 4932
53 6I7O 63 AR, XR 60S ribosomal protein L28 4932
54 6HD7 32 c 60S ribosomal protein L28 4932
55 6GQV 31 a 60S ribosomal protein L28 4932
56 6GQ1 31 a 60S ribosomal protein L28 4932
57 6GQB 31 a 60S ribosomal protein L28 4932
58 6FT6 27 a 60S ribosomal protein L28 4932
59 6ELZ 22 a 60S ribosomal protein L28 4932
60 5MC6 58 AR 60S ribosomal protein L28 4932
61 5H4P 28 a 60S ribosomal protein L28 4932
62 5M1J 39 a5 60S ribosomal protein L28 4932
63 5T62 30 n 60S ribosomal protein L28 4932
64 5T6R 29 n 60S ribosomal protein L28 4932
65 5JUO 32 FA uL15 (yeast L28) 4932
66 5JUP 32 FA uL15 (yeast L28) 4932
67 5JUS 32 FA uL15 (yeast L28) 4932
68 5JUT 32 FA uL15 (yeast L28) 4932
69 5JUU 32 FA uL15 (yeast L28) 4932
70 5JCS 48 a 60S ribosomal protein L28 4932
71 3JCT 27 a 60S ribosomal protein L28 4932
72 5GAK 12 c 60S ribosomal protein L28 4932
73 5FL8 26 a 60S ribosomal protein L28 4932
74 5APN 29 a 60S ribosomal protein L28 4932
75 5APO 29 a 60S ribosomal protein L28 4932
76 3J77 28 78 60S ribosomal protein L28 4932
77 3J78 28 78 60S ribosomal protein L28 4932
78 3J6X 30 68 60S ribosomal protein L28 4932
79 3J6Y 30 68 60S ribosomal protein L28 4932
80 4V91 29 a UL15 RIBOSOMAL PROTEIN UL15 28985
81 4V7F 17 N 60S ribosomal protein L28 4932
82 4V8Y 61 Ba 60S RIBOSOMAL PROTEIN L28 4932
83 4V8Z 61 Ba 60S RIBOSOMAL PROTEIN L28 4932
84 4V8T 27 a 60S RIBOSOMAL PROTEIN L28 4932
85 4V6I 44 BO 60S ribosomal protein rpL28 (L15p) 4932