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 95 254
95 % 54 99 319
90 % 54 99 333
70 % 54 100 372
50 % 71 147 339
40 % 72 183 260
30 % 72 183 275
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 85 302
95 % 54 87 391
90 % 54 87 408
70 % 54 88 443
50 % 71 168 288
40 % 72 170 295
30 % 72 170 319
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 95 253
95 % 54 95 342
90 % 54 96 350
70 % 54 97 383
50 % 55 98 441
40 % 56 102 453
30 % 56 102 473
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 95 260
95 % 54 95 346
90 % 54 95 359
70 % 54 97 386
50 % 71 171 278
40 % 71 171 294
30 % 71 170 322
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 91 303
95 % 57 98 341
90 % 57 98 356
70 % 57 99 387
50 % 74 156 331
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 94 261
95 % 54 94 348
90 % 54 94 360
70 % 54 95 397
50 % 71 178 264
40 % 72 179 272
30 % 140 251 200
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 67 489
95 % 54 90 368
90 % 54 91 380
70 % 72 171 254
50 % 74 175 263
40 % 74 175 281
30 % 74 175 302
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 93 268
95 % 53 93 358
90 % 53 93 373
70 % 53 94 405
50 % 53 94 457
40 % 70 168 307
30 % 70 168 328
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 95 259
95 % 54 95 340
90 % 54 95 357
70 % 54 96 393
50 % 54 96 452
40 % 54 96 480
30 % 54 96 513
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 86 295
95 % 54 86 395
90 % 54 87 405
70 % 70 157 277
50 % 72 169 286
40 % 71 169 300
30 % 72 170 320
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 86 296
95 % 54 86 394
90 % 54 86 411
70 % 54 87 445
50 % 71 169 283
40 % 72 170 296
30 % 94 193 250
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 97 252
95 % 55 99 326
90 % 55 99 337
70 % 71 168 261
50 % 73 182 249
40 % 73 182 265
30 % 73 182 283
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 87 292
95 % 48 87 388
90 % 54 94 365
70 % 54 95 396
50 % 71 170 280
40 % 71 171 290
30 % 71 171 315
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 98 240
95 % 53 98 328
90 % 53 99 334
70 % 53 99 376
50 % 71 180 251
40 % 71 180 271
30 % 71 180 289
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 95 256
95 % 54 95 344
90 % 54 96 354
70 % 54 96 392
50 % 70 171 290
40 % 70 176 288
30 % 70 176 312
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 89 280
95 % 51 89 376
90 % 51 89 395
70 % 51 91 419
50 % 69 169 289
40 % 69 170 301
30 % 69 170 324
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 93 271
95 % 53 93 363
90 % 53 94 370
70 % 53 94 410
50 % 69 161 321
40 % 70 162 326
30 % 70 163 338
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 89 279
95 % 54 89 373
90 % 54 90 383
70 % 54 90 427
50 % 70 160 320
40 % 70 166 318
30 % 72 173 309
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 68 419
95 % 38 68 566
90 % 38 68 597
70 % 38 68 648
50 % 38 68 685
40 % 38 68 713
30 % 39 69 719
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 96 251
95 % 54 96 335
90 % 54 97 344
70 % 72 182 236
50 % 72 183 240
40 % 72 183 261
30 % 72 183 276
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 63 427
95 % 40 63 578
90 % 40 63 608
70 % 40 63 658
50 % 40 63 695
40 % 44 105 483
30 % 44 105 514
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 73 398
95 % 39 73 523
90 % 39 73 553
70 % 39 73 591
50 % 39 73 625
40 % 39 75 652
30 % 39 76 677
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 100 234
95 % 54 100 317
90 % 54 101 327
70 % 54 101 370
50 % 71 177 259
40 % 71 177 279
30 % 71 177 300
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 89 289
95 % 53 89 381
90 % 53 90 390
70 % 53 90 433
50 % 69 156 333
40 % 70 169 302
30 % 70 170 323
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 87 297
95 % 54 90 367
90 % 54 91 378
70 % 54 91 415
50 % 71 173 274
40 % 72 174 286
30 % 72 176 301
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 81 314
95 % 53 81 417
90 % 53 82 436
70 % 53 82 472
50 % 53 82 504
40 % 53 82 537
30 % 53 82 562
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 245
95 % 56 95 338
90 % 56 96 346
70 % 56 96 385
50 % 69 136 357
40 % 69 136 375
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 93 264
95 % 54 93 351
90 % 54 93 366
70 % 54 94 398
50 % 71 170 282
40 % 71 170 298
30 % 71 170 321
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 96 247
95 % 54 96 334
90 % 54 96 349
70 % 54 97 381
50 % 72 174 265
40 % 72 178 274
30 % 72 179 293
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 19191
95 % 4 5 17862
90 % 4 5 17512
70 % 4 5 16335
50 % 4 5 14713
40 % 4 5 13695
30 % 4 5 12459
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 94 267
95 % 53 94 356
90 % 53 94 371
70 % 53 95 404
50 % 69 166 306
40 % 70 168 315
30 % 70 168 332
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 89 286
95 % 53 89 380
90 % 53 89 399
70 % 53 90 430
50 % 69 155 334
40 % 69 155 348
30 % 69 155 362
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 99 235
95 % 54 99 320
90 % 54 99 330
70 % 54 100 371
50 % 70 172 285
40 % 71 183 259
30 % 72 185 266
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 90 283
95 % 53 94 355
90 % 53 94 369
70 % 53 95 403
50 % 53 95 456
40 % 70 163 321
30 % 70 173 313
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 96 246
95 % 54 96 332
90 % 54 96 347
70 % 58 132 309
50 % 71 178 256
40 % 71 178 275
30 % 71 178 296
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 290
95 % 53 89 383
90 % 53 89 402
70 % 53 90 437
50 % 53 90 474
40 % 54 97 473
30 % 54 97 499
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 92 272
95 % 54 92 362
90 % 54 92 377
70 % 70 161 266
50 % 71 174 268
40 % 71 176 280
30 % 72 177 298
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 1558
95 % 9 31 2044
90 % 10 54 1113
70 % 10 57 1063
50 % 10 57 1109
40 % 10 57 1139
30 % 10 57 1180
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 25145
95 % 3 4 22136
90 % 3 4 21472
70 % 3 4 19724
50 % 13 64 1062
40 % 13 64 1096
30 % 13 64 1133
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 1719
95 % 15 31 2257
90 % 15 31 2320
70 % 16 32 2325
50 % 18 36 1830
40 % 18 36 1872
30 % 19 38 1745
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 12708
95 % 6 7 12783
90 % 6 8 10775
70 % 6 8 10671
50 % 6 8 9562
40 % 6 8 9124
30 % 6 8 8454
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 7112
95 % 9 11 7738
90 % 9 11 7701
70 % 9 11 7538
50 % 9 11 7110
40 % 9 11 6880
30 % 9 11 6454
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 89 281
95 % 54 89 377
90 % 54 90 384
70 % 70 159 273
50 % 71 172 275
40 % 139 243 199
30 % 139 243 208
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 274
95 % 54 95 343
90 % 54 96 353
70 % 54 96 391
50 % 73 183 239
40 % 73 183 255
30 % 73 185 265

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 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 5IT7 5 BB 60S ribosomal protein L3 28985
80 3JCT 2 B 60S ribosomal protein L3 4932
81 5GAK 17 F 60S ribosomal protein L3 4932
82 5FL8 2 B 60S ribosomal protein L3 4932
83 5APN 5 B 60S ribosomal protein L3 4932
84 5APO 5 B 60S ribosomal protein L3 4932
85 3J77 3 L3 60S ribosomal protein L3 4932
86 3J78 3 L3 60S ribosomal protein L3 4932
87 3J6X 6 L3 60S ribosomal protein L3 4932
88 3J6Y 6 L3 60S ribosomal protein L3 4932
89 4V91 5 B UL3 RIBOSOMAL PROTEIN UL3 28985
90 4V7F 6 C 60S ribosomal protein L3 4932
91 4V8Y 36 BB 60S RIBOSOMAL PROTEIN L3 4932
92 4V8Z 36 BB 60S RIBOSOMAL PROTEIN L3 4932
93 4V8T 2 B 60S RIBOSOMAL PROTEIN L3 4932
94 4V6I 32 BC 60S ribosomal protein rpL3 (L3p) 4932
95 4V7H 27 BC 60S ribosomal protein L3 5541
96 4V4B 22 BC 60S ribosomal protein L3 4932