6N8L

Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit


Sequence Similarity Clusters for the Entities in PDB 6N8L

Entity #1 | Chains: v
60S ribosomal export protein NMD3 protein, length: 518 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 7 11 7567
95 % 7 11 8076
90 % 7 11 8021
70 % 7 11 7811
50 % 7 11 7350
40 % 7 11 7076
30 % 7 11 6651
Entity #10 | Chains: E
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 97 275
95 % 57 100 350
90 % 57 101 361
70 % 59 104 382
50 % 60 105 439
40 % 61 109 452
30 % 61 109 472
Entity #11 | Chains: e
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 102 250
95 % 58 102 336
90 % 58 102 355
70 % 59 104 383
50 % 79 183 267
40 % 79 187 270
30 % 79 188 284
Entity #12 | Chains: F
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 101 259
95 % 58 101 348
90 % 58 101 365
70 % 59 103 391
50 % 78 179 280
40 % 78 179 292
30 % 78 178 320
Entity #13 | Chains: f
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 100 263
95 % 57 100 361
90 % 57 100 376
70 % 58 102 400
50 % 76 175 304
40 % 77 177 308
30 % 77 177 330
Entity #14 | Chains: G
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 97 309
95 % 61 104 345
90 % 61 104 362
70 % 62 106 388
50 % 79 163 331
40 % 79 165 339
30 % 79 165 357
Entity #15 | Chains: g
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 95 286
95 % 57 95 381
90 % 57 95 400
70 % 58 97 418
50 % 76 164 328
40 % 76 164 342
30 % 76 164 358
Entity #16 | Chains: I
Bud site selection protein 20 protein, length: 166 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 5 19096
95 % 3 5 18611
90 % 3 5 18280
70 % 3 5 17006
50 % 3 5 15271
40 % 3 5 14190
30 % 3 5 12916
Entity #17 | Chains: H
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 100 262
95 % 58 100 353
90 % 58 100 370
70 % 59 102 396
50 % 78 187 263
40 % 79 189 265
30 % 147 260 202
Entity #18 | Chains: h
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 105 244
95 % 58 105 324
90 % 58 105 340
70 % 59 107 376
50 % 78 182 278
40 % 79 193 254
30 % 80 195 266
Entity #19 | Chains: i
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 96 280
95 % 57 100 356
90 % 57 100 373
70 % 58 102 398
50 % 58 102 455
40 % 77 172 311
30 % 77 172 337
Entity #2 | Chains: s
Ribosomal Protein uL1 protein, length: 217 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | Chains: j
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 102 254
95 % 58 102 339
90 % 58 102 357
70 % 65 143 307
50 % 78 187 257
40 % 78 187 271
30 % 78 187 287
Entity #21 | Chains: k
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 95 288
95 % 57 95 386
90 % 57 95 401
70 % 58 97 421
50 % 58 97 472
40 % 59 104 469
30 % 59 104 483
Entity #22 | Chains: L
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 99 270
95 % 57 99 365
90 % 57 99 381
70 % 58 101 403
50 % 58 101 458
40 % 77 177 300
30 % 77 177 325
Entity #23 | Chains: l
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 59 99 265
95 % 59 99 358
90 % 59 99 372
70 % 77 171 270
50 % 78 183 265
40 % 78 185 274
30 % 79 186 294
Entity #24 | Chains: M
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 101 260
95 % 58 101 347
90 % 58 101 363
70 % 59 103 390
50 % 59 103 450
40 % 59 103 476
30 % 59 103 491
Entity #25 | Chains: p
60S ribosomal protein L43-A protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 92 299
95 % 58 92 394
90 % 58 92 408
70 % 59 94 429
50 % 78 178 283
40 % 79 179 291
30 % 101 202 253
Entity #26 | Chains: N
60S ribosomal protein L15-A protein, length: 204 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 103 253
95 % 60 106 322
90 % 60 106 337
70 % 78 177 262
50 % 80 191 249
40 % 80 191 262
30 % 80 191 276
Entity #27 | Chains: u
Ribosome biogenesis protein RLP24 protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 13 5823
95 % 3 13 6610
90 % 3 13 6622
70 % 3 13 6541
50 % 3 13 6243
40 % 3 13 6061
30 % 3 13 5781
Entity #28 | Chains: O
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 291
95 % 52 93 389
90 % 58 100 366
70 % 59 102 392
50 % 78 179 276
40 % 78 180 284
30 % 78 180 312
Entity #29 | Chains: P
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 104 246
95 % 57 104 331
90 % 58 106 334
70 % 58 106 377
50 % 78 189 251
40 % 78 189 266
30 % 78 189 281
Entity #3 | Chains: A
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 95 281
95 % 58 95 377
90 % 59 97 385
70 % 77 168 273
50 % 78 181 273
40 % 146 252 198
30 % 146 252 208
Entity #30 | Chains: Q
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 101 257
95 % 58 101 344
90 % 59 103 352
70 % 59 103 387
50 % 77 180 287
40 % 77 185 282
30 % 77 185 308
Entity #31 | Chains: R
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 55 95 282
95 % 55 95 376
90 % 55 95 393
70 % 56 98 408
50 % 77 179 282
40 % 77 180 289
30 % 77 180 316
Entity #32 | Chains: S
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 99 274
95 % 57 99 364
90 % 58 101 369
70 % 58 101 402
50 % 76 170 316
40 % 77 171 318
30 % 77 172 339
Entity #33 | Chains: T
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 95 284
95 % 58 95 379
90 % 59 97 382
70 % 59 97 415
50 % 77 169 313
40 % 77 175 310
30 % 79 182 310
Entity #34 | Chains: U
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 40 72 433
95 % 40 72 572
90 % 40 72 599
70 % 41 73 614
50 % 41 73 659
40 % 41 73 692
30 % 42 74 691
Entity #35 | Chains: V
60S ribosomal protein L23-A protein, length: 137 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 102 251
95 % 58 102 338
90 % 59 104 346
70 % 79 191 227
50 % 79 192 245
40 % 79 192 258
30 % 79 192 272
Entity #36 | Chains: W
Ribosome assembly factor MRT4 protein, length: 236 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 11 7627
95 % 3 11 8199
90 % 3 11 8140
70 % 3 11 7929
50 % 3 11 7455
40 % 3 11 7188
30 % 3 11 6746
Entity #37 | Chains: X
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 41 77 399
95 % 41 77 528
90 % 42 78 543
70 % 42 78 574
50 % 42 78 616
40 % 42 80 630
30 % 42 81 645
Entity #38 | Chains: Y
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 106 242
95 % 58 106 319
90 % 59 108 326
70 % 59 108 372
50 % 79 190 247
40 % 79 190 260
30 % 79 190 275
Entity #39 | Chains: y
Eukaryotic translation initiation factor 6 protein, length: 245 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 31 1791
95 % 13 31 2341
90 % 13 31 2393
70 % 14 32 2381
50 % 16 36 1911
40 % 16 36 1948
30 % 17 38 1836
Entity #4 | Chains: a
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 93 297
95 % 58 96 373
90 % 59 98 377
70 % 59 98 406
50 % 78 182 271
40 % 79 183 276
30 % 79 185 296
Entity #40 | Chains: Z
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 95 287
95 % 57 95 385
90 % 58 97 388
70 % 58 97 420
50 % 76 165 326
40 % 77 178 295
30 % 78 180 317
Entity #41 | Chains: z
UPF0642 protein YBL028C protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 8 10852
95 % 3 8 11955
90 % 3 8 11807
70 % 3 8 11274
50 % 3 8 10340
40 % 3 8 9906
30 % 3 8 9168
Entity #42 | Chains: D
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 91 304
95 % 58 93 390
90 % 58 93 404
70 % 59 95 427
50 % 78 177 286
40 % 79 179 288
30 % 79 179 314
Entity #43 | Chains: J
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 35 73 475
95 % 58 96 372
90 % 59 98 380
70 % 79 180 252
50 % 81 184 261
40 % 81 184 275
30 % 81 184 299
Entity #44 | Chains: q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 92 296
95 % 58 92 393
90 % 59 94 395
70 % 77 168 277
50 % 79 175 296
40 % 79 176 302
30 % 79 176 327
Entity #45 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 87 315
95 % 57 87 423
90 % 58 89 434
70 % 58 89 462
50 % 58 89 496
40 % 58 89 531
30 % 58 89 552
Entity #46 | Chains: 1
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 #47 | Chains: 2
5S rRNA rna, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #48 | Chains: 3
5.8S rRNA rna, length: 158 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #5 | Chains: B
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 99 276
95 % 58 101 346
90 % 59 103 351
70 % 59 103 389
50 % 80 192 244
40 % 80 192 256
30 % 80 194 268
Entity #6 | Chains: b
Nucleolar GTP-binding protein 1 protein, length: 647 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 12 6668
95 % 3 12 6780
90 % 3 12 6798
70 % 3 12 6697
50 % 3 12 6395
40 % 3 12 6211
30 % 3 12 5906
Entity #7 | Chains: C
60S ribosomal protein L4-A protein, length: 362 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 101 256
95 % 58 105 321
90 % 58 105 336
70 % 59 107 374
50 % 76 154 341
40 % 79 192 257
30 % 79 192 270
Entity #8 | Chains: c
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 60 101 255
95 % 60 101 341
90 % 61 103 348
70 % 61 103 385
50 % 74 143 355
40 % 74 143 368
30 % 74 143 386
Entity #9 | Chains: d
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 99 266
95 % 58 99 359
90 % 58 99 375
70 % 59 101 399
50 % 78 179 281
40 % 78 179 293
30 % 78 179 318

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 46 BH, DH 60S ribosomal protein L9-A 4932
2 4U4R 46 L9, l9 60S ribosomal protein L9-A 4932
3 4U3U 46 L9, l9 60S ribosomal protein L9-A 4932
4 5TBW 11 CK, q 60S ribosomal protein L9-A 4932
5 4U3M 46 L9, l9 60S ribosomal protein L9-A 4932
6 4U3N 46 L9, l9 60S ribosomal protein L9-A 4932
7 4U52 46 L9, l9 60S ribosomal protein L9-A 4932
8 4U4Q 46 L9, l9 60S ribosomal protein L9-A 4932
9 4U6F 46 L9, l9 60S ribosomal protein L9-A 4932
10 4U4U 46 L9, l9 60S ribosomal protein L9-A 4932
11 4U4Z 46 L9, l9 60S ribosomal protein L9-A 4932
12 4U4Y 46 L9, l9 60S ribosomal protein L9-A 4932
13 4U4N 46 L9, l9 60S ribosomal protein L9-A 4932
14 4U55 46 L9, l9 60S ribosomal protein L9-A 4932
15 5DAT 46 L9, l9 60S ribosomal protein L9-A 4932
16 5I4L 46 L9, l9 60S ribosomal protein L9-A 4932
17 4U51 46 L9, l9 60S ribosomal protein L9-A 4932
18 6HHQ 11 CK, q 60S ribosomal protein L9-A 4932
19 5OBM 11 L9, l9 60S ribosomal protein L9-A 4932
20 4U53 46 L9, l9 60S ribosomal protein L9-A 4932
21 5ON6 11 CK, q 60S ribosomal protein L9-A 4932
22 4U50 46 L9, l9 60S ribosomal protein L9-A 4932
23 5NDV 11 L9, l9 60S ribosomal protein L9-A 4932
24 5LYB 46 L9, l9 60S ribosomal protein L9-A 4932
25 4U56 46 L9, l9 60S ribosomal protein L9-A 4932
26 5TGA 46 L9, l9 60S ribosomal protein L9-A 4932
27 5MEI 11 CK, q 60S ribosomal protein L9-A 4932
28 5FCJ 46 L9, l9 60S ribosomal protein L9-A 4932
29 4U4O 46 L9, l9 60S ribosomal protein L9-A 4932
30 5DGV 46 L9, l9 60S ribosomal protein L9-A 4932
31 5DGE 46 L9, l9 60S ribosomal protein L9-A 4932
32 5NDW 34 L9, l9 60S ribosomal protein L9-A 4932
33 5NDG 46 L9, l9 60S ribosomal protein L9-A 4932
34 5FCI 46 L9, l9 60S ribosomal protein L9-A 4932
35 5DC3 46 L9, l9 60S ribosomal protein L9-A 4932
36 5DGF 46 L9, l9 60S ribosomal protein L9-A 4932
37 5TGM 46 L9, l9 60S ribosomal protein L9-A 4932
38 4V7R 40 BI, DI 60S ribosomal protein L9-A 4932
39 6T83 44 Hy, Ka 60S ribosomal protein L9-A 4932
40 6T7T 44 LH 60S ribosomal protein L9-A 4932
41 6T7I 44 LH 60S ribosomal protein L9-A 4932
42 6T4Q 43 LH 60S ribosomal protein L9-A 4932
43 6SV4 11 AD, XD, zD 60S ribosomal protein L9-A 4932
44 6SNT 44 o 60S ribosomal protein L9-A 4932
45 6S47 11 AK 60S ribosomal protein L9-A 4932
46 6RZZ 6 F 60S ribosomal protein L9-A 4932
47 6S05 6 F 60S ribosomal protein L9-A 4932
48 6RI5 6 F 60S ribosomal protein L9-A 4932
49 6R84 9 7 60S ribosomal protein L9-A 4932
50 6R86 8 7 60S ribosomal protein L9-A 4932
51 6R87 8 7 60S ribosomal protein L9-A 4932
52 6QTZ 6 F 60S ribosomal protein L9-A 4932
53 6QT0 6 F 60S ribosomal protein L9-A 4932
54 6QIK 6 F 60S ribosomal protein L9-A 4932
55 6Q8Y 5 AD 60S ribosomal protein L9-A 4932
56 6N8J 17 H 60S ribosomal protein L9-A 4932
57 6N8K 17 H 60S ribosomal protein L9-A 4932
58 6N8L 17 H 60S ribosomal protein L9-A 4932
59 6N8M 12 K 60S ribosomal protein L9-A 4932
60 6N8N 15 K 60S ribosomal protein L9-A 4932
61 6N8O 16 K 60S ribosomal protein L9-A 4932
62 6I7O 11 AD, XD 60S ribosomal protein L9-A 4932
63 6HD7 15 L 60S ribosomal protein L9-A 4932
64 6GQV 13 H 60S ribosomal protein L9-A 4932
65 6GQ1 13 H 60S ribosomal protein L9-A 4932
66 6GQB 13 H 60S ribosomal protein L9-A 4932
67 6FT6 9 H 60S ribosomal protein L9-A 4932
68 5Z3G 12 L 60S ribosomal protein L9-A 4932
69 6EM1 23 H 60S ribosomal protein L9-A 4932
70 6EM5 29 H 60S ribosomal protein L9-A Backbone model 4932
71 6ELZ 30 H 60S ribosomal protein L9-A 4932
72 5MC6 44 AD 60S ribosomal protein L9-A 4932
73 5H4P 11 H 60S ribosomal protein L9-A 4932
74 5M1J 53 H5 60S ribosomal protein L9-A 4932
75 5T62 12 K 60S ribosomal protein L9-A 4932
76 5T6R 11 K 60S ribosomal protein L9-A 4932
77 5JUO 13 M uL6 (yeast L9) 4932
78 5JUP 13 M uL6 (yeast L9) 4932
79 5JUS 13 M uL6 (yeast L9) 4932
80 5JUT 13 M uL6 (yeast L9) 4932
81 5JUU 13 M uL6 (yeast L9) 4932
82 5JCS 15 H 60S ribosomal protein L9-A 4932
83 3JCT 8 H 60S ribosomal protein L9-A 4932
84 5GAK 29 L 60S ribosomal protein L9-A 4932
85 5FL8 8 H Rpl9ap 4932
86 5APN 11 H 60S ribosomal protein L9-A 4932
87 5APO 11 H 60S ribosomal protein L9-A 4932
88 3J77 9 L9 60S ribosomal protein L9 4932
89 3J78 9 L9 60S ribosomal protein L9 4932
90 3J6X 12 L9 60S ribosomal protein L9 4932
91 3J6Y 12 L9 60S ribosomal protein L9 4932
92 4V91 11 H UL6 RIBOSOMAL PROTEIN UL6 28985
93 4V7F 9 F 60S ribosomal protein L9 4932
94 4V8Y 42 BH 60S RIBOSOMAL PROTEIN L9-A 4932
95 4V8Z 42 BH 60S RIBOSOMAL PROTEIN L9-A 4932
96 4V8T 8 H 60S RIBOSOMAL PROTEIN L9-A 4932
97 3J16 6 F 60S ribosomal protein L6 4932
98 4V6I 36 BF 60S ribosomal protein rpL9 (L6p) 4932
99 4V7H 32 BH 60S ribosomal protein L9(A) 5541
100 4V4B 27 BH 60S ribosomal protein L9-A 4932