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 95 271
95 % 54 99 339
90 % 54 99 349
70 % 54 100 382
50 % 71 147 341
40 % 74 185 260
30 % 74 185 282
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 85 314
95 % 54 87 411
90 % 54 87 426
70 % 54 88 454
50 % 73 170 294
40 % 74 172 294
30 % 74 172 320
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 95 267
95 % 54 95 363
90 % 54 96 370
70 % 54 97 395
50 % 55 98 451
40 % 56 102 461
30 % 56 102 477
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 268
95 % 54 95 357
90 % 54 95 372
70 % 54 97 390
50 % 73 173 281
40 % 73 173 293
30 % 73 172 325
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 91 316
95 % 57 98 362
90 % 57 98 374
70 % 57 99 403
50 % 74 156 333
40 % 74 158 341
30 % 74 158 359
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 94 274
95 % 54 94 365
90 % 54 94 377
70 % 54 95 404
50 % 73 180 268
40 % 74 181 272
30 % 142 253 203
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 67 500
95 % 54 90 384
90 % 54 91 395
70 % 74 173 257
50 % 76 177 266
40 % 76 177 284
30 % 76 177 307
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 93 279
95 % 53 93 378
90 % 53 93 389
70 % 53 94 414
50 % 53 94 466
40 % 72 170 308
30 % 72 170 331
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 95 269
95 % 54 95 360
90 % 54 95 373
70 % 54 96 397
50 % 54 96 459
40 % 54 96 488
30 % 54 96 521
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 86 307
95 % 54 86 413
90 % 54 87 425
70 % 72 159 278
50 % 74 171 290
40 % 73 171 302
30 % 74 172 323
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 86 308
95 % 54 86 415
90 % 54 86 431
70 % 54 87 459
50 % 73 171 285
40 % 74 172 295
30 % 96 195 249
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 % 54 97 257
95 % 55 99 343
90 % 55 99 353
70 % 73 170 263
50 % 75 184 249
40 % 75 184 264
30 % 75 184 287
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 87 305
95 % 48 87 409
90 % 54 94 379
70 % 54 95 405
50 % 73 172 282
40 % 73 173 292
30 % 73 173 318
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 98 251
95 % 53 98 342
90 % 53 99 346
70 % 53 99 384
50 % 73 182 255
40 % 73 182 270
30 % 73 182 293
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 95 270
95 % 54 95 361
90 % 54 96 368
70 % 54 96 401
50 % 72 173 293
40 % 72 178 287
30 % 72 178 310
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 89 289
95 % 51 89 396
90 % 51 89 414
70 % 51 91 429
50 % 71 171 292
40 % 71 172 305
30 % 71 172 330
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 93 282
95 % 53 93 379
90 % 53 94 387
70 % 53 94 416
50 % 71 163 321
40 % 72 164 326
30 % 72 165 343
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 89 287
95 % 54 89 391
90 % 54 90 400
70 % 54 90 433
50 % 72 162 320
40 % 72 168 321
30 % 74 175 312
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 68 443
95 % 38 68 597
90 % 38 68 622
70 % 38 68 665
50 % 38 68 699
40 % 38 68 725
30 % 39 69 734
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 96 259
95 % 54 96 351
90 % 54 97 358
70 % 74 184 235
50 % 74 185 248
40 % 74 185 261
30 % 74 185 284
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 63 448
95 % 40 63 605
90 % 40 63 630
70 % 40 63 671
50 % 40 63 704
40 % 46 107 486
30 % 46 107 512
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 73 415
95 % 39 73 544
90 % 39 73 566
70 % 39 73 600
50 % 39 73 640
40 % 39 75 661
30 % 39 76 691
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 100 246
95 % 54 100 334
90 % 54 101 340
70 % 54 101 376
50 % 73 182 253
40 % 73 182 268
30 % 73 182 291
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 89 294
95 % 53 89 399
90 % 53 90 404
70 % 53 90 438
50 % 71 158 328
40 % 72 171 306
30 % 73 173 322
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 87 309
95 % 54 90 385
90 % 54 91 396
70 % 54 91 423
50 % 73 175 274
40 % 74 176 285
30 % 74 178 306
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 81 330
95 % 53 81 439
90 % 53 82 452
70 % 53 82 481
50 % 53 82 515
40 % 53 82 556
30 % 53 82 577
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 263
95 % 56 95 352
90 % 56 96 359
70 % 56 96 393
50 % 76 181 254
40 % 76 181 269
30 % 76 181 292
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 93 276
95 % 54 93 372
90 % 54 93 384
70 % 54 94 408
50 % 73 172 283
40 % 73 172 296
30 % 73 172 324
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 258
95 % 54 96 353
90 % 54 96 364
70 % 54 97 394
50 % 74 176 269
40 % 74 180 276
30 % 74 181 295
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 19563
95 % 4 5 17668
90 % 4 5 17355
70 % 4 5 16180
50 % 4 5 14589
40 % 4 5 13567
30 % 4 5 12355
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 94 278
95 % 53 94 371
90 % 53 94 386
70 % 53 95 410
50 % 71 168 307
40 % 72 170 318
30 % 72 170 339
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 89 298
95 % 53 89 400
90 % 53 89 418
70 % 53 90 442
50 % 71 157 332
40 % 71 157 346
30 % 71 157 363
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 99 247
95 % 54 99 336
90 % 54 99 345
70 % 54 100 379
50 % 72 174 289
40 % 73 185 258
30 % 74 187 272
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 94 369
90 % 53 94 383
70 % 53 95 409
50 % 53 95 464
40 % 72 165 322
30 % 72 175 315
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 96 262
95 % 54 96 350
90 % 54 96 369
70 % 60 134 315
50 % 73 180 259
40 % 73 180 277
30 % 73 180 299
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 89 404
90 % 53 89 419
70 % 53 90 444
50 % 53 90 485
40 % 54 97 484
30 % 54 97 509
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 92 281
95 % 54 92 375
90 % 54 92 392
70 % 72 164 269
50 % 73 176 271
40 % 73 178 282
30 % 74 179 301
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 1620
95 % 9 31 2122
90 % 10 54 1135
70 % 10 57 1087
50 % 10 57 1131
40 % 10 57 1166
30 % 10 57 1204
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 27782
95 % 3 4 22323
90 % 3 4 22204
70 % 3 4 19938
50 % 15 66 1047
40 % 15 66 1090
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 1725
95 % 15 31 2252
90 % 15 31 2305
70 % 16 32 2270
50 % 18 36 1824
40 % 18 36 1873
30 % 19 38 1761
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 12757
95 % 6 7 12960
90 % 6 8 10897
70 % 6 8 10817
50 % 6 8 9683
40 % 6 8 9454
30 % 6 8 8566
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 7157
95 % 9 11 7897
90 % 9 11 7860
70 % 9 11 7666
50 % 9 11 7198
40 % 9 11 6955
30 % 9 11 6528
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 89 293
95 % 54 89 394
90 % 54 90 401
70 % 72 161 274
50 % 73 174 276
40 % 141 245 198
30 % 141 245 210
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 285
95 % 54 95 359
90 % 54 96 366
70 % 54 96 400
50 % 75 185 245
40 % 75 185 257
30 % 75 187 270

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 40 BB, DB 60S ribosomal protein L3 4932
2 4U4R 40 L3, l3 60S ribosomal protein L3 4932
3 4U3U 40 L3, l3 60S ribosomal protein L3 4932
4 5TBW 5 CE, k 60S ribosomal protein L3 4932
5 4U3M 40 L3, l3 60S ribosomal protein L3 4932
6 4U3N 40 L3, l3 60S ribosomal protein L3 4932
7 4U52 40 L3, l3 60S ribosomal protein L3 4932
8 4U4Q 40 L3, l3 60S ribosomal protein L3 4932
9 4U6F 40 L3, l3 60S ribosomal protein L3 4932
10 4U4U 40 L3, l3 60S ribosomal protein L3 4932
11 4U4Z 40 L3, l3 60S ribosomal protein L3 4932
12 4U4Y 40 L3, l3 60S ribosomal protein L3 4932
13 4U4N 40 L3, l3 60S ribosomal protein L3 4932
14 4U55 40 L3, l3 60S ribosomal protein L3 4932
15 5DAT 40 L3, l3 60S ribosomal protein L3 4932
16 5I4L 40 L3, l3 60S ribosomal protein L3 4932
17 4U51 40 L3, l3 60S ribosomal protein L3 4932
18 6HHQ 5 CE, k 60S ribosomal protein L3 4932
19 5OBM 5 L3, l3 60S ribosomal protein L3 4932
20 4U53 40 L3, l3 60S ribosomal protein L3 4932
21 5ON6 5 CE, k 60S ribosomal protein L3 4932
22 4U50 40 L3, l3 60S ribosomal protein L3 4932
23 5NDV 5 L3, l3 60S ribosomal protein L3 4932
24 5LYB 40 L3, l3 60S ribosomal protein L3 4932
25 4U56 40 L3, l3 60S ribosomal protein L3 4932
26 5TGA 40 L3, l3 60S ribosomal protein L3 4932
27 5MEI 5 CE, k 60S ribosomal protein L3 4932
28 5FCJ 40 L3, l3 60S ribosomal protein L3 There is one mutation (W255C). The original sequence is: SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDT PPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVL VHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRK THRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDF IMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL 4932
29 4U4O 40 L3, l3 60S ribosomal protein L3 4932
30 5DGV 40 L3, l3 60S ribosomal protein L3 4932
31 5DGE 40 L3, l3 60S ribosomal protein L3 4932
32 5NDW 28 L3, l3 60S ribosomal protein L3 4932
33 5NDG 40 L3, l3 60S ribosomal protein L3 4932
34 5FCI 40 L3, l3 60S ribosomal protein L3 4932
35 5DC3 40 L3, l3 60S ribosomal protein L3 4932
36 5DGF 40 L3, l3 60S ribosomal protein L3 4932
37 5TGM 40 L3, l3 60S ribosomal protein L3 4932
38 4V7R 34 BC, DC 60S ribosomal protein L3 4932
39 6S47 5 AE 60S ribosomal protein L3 4932
40 6RZZ 3 C 60S ribosomal protein L3 4932
41 6S05 3 C 60S ribosomal protein L3 4932
42 6RI5 3 C 60S ribosomal protein L3 4932
43 6R84 42 F 60S ribosomal protein L3 4932
44 6R86 40 F 60S ribosomal protein L3 4932
45 6R87 41 F 60S ribosomal protein L3 4932
46 6QTZ 3 C 60S ribosomal protein L3 4932
47 6QT0 3 C 60S ribosomal protein L3 4932
48 6QIK 3 C 60S ribosomal protein L3 4932
49 6Q8Y 38 BA 60S ribosomal protein L3 4932
50 6N8J 5 B 60S ribosomal protein L3 4932
51 6N8K 5 B 60S ribosomal protein L3 4932
52 6N8L 5 B 60S ribosomal protein L3 4932
53 6N8M 6 E 60S ribosomal protein L3 4932
54 6N8N 9 E 60S ribosomal protein L3 4932
55 6N8O 10 E 60S ribosomal protein L3 4932
56 6I7O 5 BA, YA 60S ribosomal protein L3 4932
57 6HD7 9 F 60S ribosomal protein L3 4932
58 6GQV 7 B 60S ribosomal protein L3 4932
59 6GQ1 7 B 60S ribosomal protein L3 4932
60 6GQB 7 B 60S ribosomal protein L3 4932
61 6FT6 3 B 60S ribosomal protein L3 4932
62 5Z3G 6 F 60S ribosomal protein L3 4932
63 6C0F 5 B 60S ribosomal protein L3 4932
64 6EM1 16 B 60S ribosomal protein L3 4932
65 6EM4 11 B 60S ribosomal protein L3 Backbone model 4932
66 6EM5 27 B 60S ribosomal protein L3 Backbone model 4932
67 6ELZ 28 B 60S ribosomal protein L3 4932
68 5MC6 67 BA 60S ribosomal protein L3 4932
69 5H4P 5 B 60S ribosomal protein L3 4932
70 5M1J 42 B5 60S ribosomal protein L3 4932
71 5T62 6 E 60S ribosomal protein L3 4932
72 5T6R 5 E 60S ribosomal protein L3 4932
73 5JUO 7 G uL3 (yeast L3) 4932
74 5JUP 7 G uL3 (yeast L3) 4932
75 5JUS 7 G uL3 (yeast L3) 4932
76 5JUT 7 G uL3 (yeast L3) 4932
77 5JUU 7 G uL3 (yeast L3) 4932
78 5JCS 3 B 60S ribosomal protein L3 4932
79 3JCT 2 B 60S ribosomal protein L3 4932
80 5GAK 17 F 60S ribosomal protein L3 4932
81 5FL8 2 B 60S ribosomal protein L3 4932
82 5APN 5 B 60S ribosomal protein L3 4932
83 5APO 5 B 60S ribosomal protein L3 4932
84 3J77 3 L3 60S ribosomal protein L3 4932
85 3J78 3 L3 60S ribosomal protein L3 4932
86 3J6X 6 L3 60S ribosomal protein L3 4932
87 3J6Y 6 L3 60S ribosomal protein L3 4932
88 4V91 5 B UL3 RIBOSOMAL PROTEIN UL3 28985
89 4V7F 6 C 60S ribosomal protein L3 4932
90 4V8Y 36 BB 60S RIBOSOMAL PROTEIN L3 4932
91 4V8Z 36 BB 60S RIBOSOMAL PROTEIN L3 4932
92 4V8T 2 B 60S RIBOSOMAL PROTEIN L3 4932
93 4V6I 32 BC 60S ribosomal protein rpL3 (L3p) 4932
94 4V7H 27 BC 60S ribosomal protein L3 5541
95 4V4B 22 BC 60S ribosomal protein L3 4932