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 % 58 99 258
95 % 58 103 324
90 % 58 103 337
70 % 59 105 373
50 % 76 152 336
40 % 79 190 247
30 % 79 190 267
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 89 304
95 % 58 91 391
90 % 58 91 404
70 % 59 93 422
50 % 78 175 281
40 % 79 177 290
30 % 79 177 315
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 55 96 269
95 % 58 99 345
90 % 58 100 351
70 % 59 102 380
50 % 60 103 436
40 % 61 107 449
30 % 61 107 466
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 99 257
95 % 58 99 344
90 % 58 99 357
70 % 59 101 384
50 % 78 177 277
40 % 78 177 294
30 % 78 176 319
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 95 308
95 % 61 102 349
90 % 61 102 359
70 % 62 104 388
50 % 79 161 325
40 % 79 163 334
30 % 79 163 350
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 98 263
95 % 58 98 354
90 % 58 98 366
70 % 59 100 393
50 % 78 185 258
40 % 79 187 258
30 % 147 258 198
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 35 71 482
95 % 58 94 374
90 % 59 96 380
70 % 79 178 253
50 % 81 182 259
40 % 81 182 274
30 % 81 182 298
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 97 268
95 % 57 97 363
90 % 57 97 376
70 % 58 99 401
50 % 76 168 310
40 % 77 175 300
30 % 77 175 321
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 99 259
95 % 58 99 350
90 % 58 99 360
70 % 59 101 383
50 % 59 101 446
40 % 59 101 471
30 % 59 101 491
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 90 297
95 % 58 90 397
90 % 59 92 396
70 % 77 166 270
50 % 79 173 291
40 % 79 174 299
30 % 79 174 320
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 % 58 90 300
95 % 58 90 398
90 % 58 90 410
70 % 59 92 426
50 % 78 176 278
40 % 79 177 291
30 % 101 200 247
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 % 58 101 253
95 % 60 104 323
90 % 60 104 338
70 % 78 175 262
50 % 80 189 243
40 % 80 189 255
30 % 147 259 199
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 91 295
95 % 52 91 393
90 % 58 98 363
70 % 59 100 391
50 % 78 177 273
40 % 78 178 288
30 % 78 178 312
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 102 245
95 % 57 102 331
90 % 58 104 336
70 % 58 104 377
50 % 78 187 246
40 % 78 187 259
30 % 78 187 281
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 99 260
95 % 58 99 347
90 % 59 101 349
70 % 59 101 389
50 % 77 178 285
40 % 77 183 280
30 % 77 183 304
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 55 93 282
95 % 55 93 376
90 % 55 93 392
70 % 56 96 413
50 % 76 176 282
40 % 76 177 296
30 % 76 177 318
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 97 271
95 % 57 97 366
90 % 58 99 362
70 % 58 99 402
50 % 76 168 312
40 % 77 169 316
30 % 77 170 335
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 93 286
95 % 58 93 378
90 % 59 95 384
70 % 59 95 418
50 % 77 167 311
40 % 77 173 312
30 % 79 180 302
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 41 71 426
95 % 41 71 572
90 % 41 71 595
70 % 42 72 608
50 % 42 72 655
40 % 42 72 684
30 % 43 73 697
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 % 58 100 256
95 % 58 100 342
90 % 59 102 342
70 % 79 189 224
50 % 79 190 237
40 % 79 190 250
30 % 79 190 269
Entity #31 | Chains: j
60S ribosomal protein L24-A protein, length: 155 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 41 64 443
95 % 43 66 587
90 % 43 66 609
70 % 44 67 639
50 % 44 67 676
40 % 50 111 466
30 % 50 111 486
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 42 76 393
95 % 42 76 528
90 % 43 77 545
70 % 43 77 578
50 % 43 77 611
40 % 43 79 628
30 % 43 80 649
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 104 241
95 % 58 104 322
90 % 59 106 331
70 % 59 106 371
50 % 78 184 255
40 % 78 184 269
30 % 78 184 291
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 93 288
95 % 57 93 382
90 % 58 95 389
70 % 58 95 419
50 % 76 163 323
40 % 77 176 297
30 % 78 178 316
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 91 298
95 % 58 94 372
90 % 59 96 378
70 % 59 96 411
50 % 78 180 268
40 % 79 181 277
30 % 79 183 296
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 85 315
95 % 57 85 425
90 % 58 87 437
70 % 58 87 463
50 % 58 87 499
40 % 58 87 530
30 % 58 87 553
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 60 99 255
95 % 60 99 340
90 % 61 101 341
70 % 61 101 379
50 % 74 141 350
40 % 74 141 363
30 % 74 141 379
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 97 266
95 % 58 97 359
90 % 58 97 372
70 % 59 99 398
50 % 78 177 276
40 % 78 177 293
30 % 78 177 317
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 100 252
95 % 58 100 343
90 % 58 100 354
70 % 59 102 382
50 % 79 181 264
40 % 79 185 266
30 % 79 186 283
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 18420
95 % 4 5 17672
90 % 4 5 17858
70 % 4 5 16170
50 % 4 5 14611
40 % 4 5 13570
30 % 4 5 12340
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 98 264
95 % 57 98 356
90 % 57 98 368
70 % 58 100 395
50 % 76 173 298
40 % 77 175 308
30 % 77 175 331
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 93 292
95 % 57 93 388
90 % 57 93 401
70 % 58 95 421
50 % 76 162 326
40 % 76 162 340
30 % 76 162 356
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 103 243
95 % 58 103 327
90 % 58 103 339
70 % 59 105 375
50 % 77 179 280
40 % 78 190 245
30 % 79 192 258
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 94 287
95 % 57 98 360
90 % 57 98 373
70 % 58 100 399
50 % 58 100 456
40 % 77 170 314
30 % 77 180 311
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 100 254
95 % 58 100 338
90 % 58 100 352
70 % 65 141 304
50 % 78 185 252
40 % 78 185 267
30 % 78 185 288
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 57 93 290
95 % 57 93 384
90 % 57 93 398
70 % 58 95 420
50 % 58 95 468
40 % 59 102 460
30 % 59 102 477
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 59 97 267
95 % 59 97 361
90 % 59 97 374
70 % 77 168 267
50 % 78 181 263
40 % 78 183 271
30 % 79 184 292
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 12 34 1375
95 % 13 35 1755
90 % 14 58 1037
70 % 14 61 1016
50 % 14 61 1043
40 % 14 61 1088
30 % 14 61 1133
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 27474
95 % 3 4 21824
90 % 3 4 21220
70 % 3 4 19546
50 % 15 66 1053
40 % 15 66 1099
30 % 15 66 1145
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 1750
95 % 15 31 2277
90 % 15 31 2357
70 % 16 32 2306
50 % 18 36 1829
40 % 18 36 1892
30 % 19 38 1782
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 13305
95 % 6 7 12946
90 % 6 8 11147
70 % 6 8 10702
50 % 6 8 9877
40 % 6 8 9372
30 % 6 8 8702
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 7277
95 % 9 11 8057
90 % 9 11 8015
70 % 9 11 7799
50 % 9 11 7342
40 % 9 11 7071
30 % 9 11 6654
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 93 283
95 % 58 93 377
90 % 59 95 386
70 % 77 166 271
50 % 78 179 270
40 % 146 250 193
30 % 146 250 203
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 97 279
95 % 58 99 348
90 % 59 101 348
70 % 59 101 387
50 % 80 190 233
40 % 80 190 244
30 % 80 192 256

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 78 Bo, Do 60S ribosomal protein L42-A 4932
2 4U4R 78 Q2, q2 60S ribosomal protein L42-A 4932
3 4U3U 78 Q2, q2 60S ribosomal protein L42-A 4932
4 5TBW 43 AP, DQ 60S ribosomal protein L42-A 4932
5 4U3M 78 Q2, q2 60S ribosomal protein L42-A 4932
6 4U3N 78 Q2, q2 60S ribosomal protein L42-A 4932
7 4U52 78 Q2, q2 60S ribosomal protein L42-A 4932
8 4U4Q 78 Q2, q2 60S ribosomal protein L42-A 4932
9 4U6F 78 Q2, q2 60S ribosomal protein L42-A 4932
10 4U4U 78 Q2, q2 60S ribosomal protein L42-A 4932
11 4U4Z 78 Q2, q2 60S ribosomal protein L42-A 4932
12 4U4Y 78 Q2, q2 60S ribosomal protein L42-A 4932
13 4U4N 78 Q2, q2 60S ribosomal protein L42-A 4932
14 4U55 78 Q2, q2 60S ribosomal protein L42-A 4932
15 5DAT 78 Q2, q2 60S ribosomal protein L42-A 4932
16 5I4L 78 Q2, q2 60S ribosomal protein L42-A 4932
17 4U51 78 Q2, q2 60S ribosomal protein L42-A 4932
18 6HHQ 43 AP, DQ 60S ribosomal protein L42-A 4932
19 5OBM 43 Q2, q2 60S ribosomal protein L42-A 4932
20 4U53 78 Q2, q2 60S ribosomal protein L42-A 4932
21 5ON6 44 AP, DQ 60S ribosomal protein L42-A 4932
22 4U50 78 Q2, q2 60S ribosomal protein L42-A 4932
23 5NDV 43 Q2, q2 60S ribosomal protein L42-A 4932
24 5LYB 78 Q2, q2 60S ribosomal protein L42-A 4932
25 4U56 78 Q2, q2 60S ribosomal protein L42-A 4932
26 5TGA 78 Q2, q2 60S ribosomal protein L42-A 4932
27 5MEI 44 AP, DQ 60S ribosomal protein L42-A 4932
28 5FCJ 78 Q2, q2 60S ribosomal protein L42-A 4932
29 4U4O 78 Q2, q2 60S ribosomal protein L42-A 4932
30 5DGV 78 Q2, q2 60S ribosomal protein L42-A 4932
31 5DGE 78 Q2, q2 60S ribosomal protein L42-A 4932
32 5NDW 66 Q2, q2 60S ribosomal protein L42-A 4932
33 5NDG 78 Q2, q2 60S ribosomal protein L42-A 4932
34 5FCI 78 Q2, q2 60S ribosomal protein L42-A 4932
35 5DC3 78 Q2, q2 60S ribosomal protein L42-A 4932
36 5DGF 78 Q2, q2 60S ribosomal protein L42-A 4932
37 5TGM 78 Q2, q2 60S ribosomal protein L42-A 4932
38 4V7R 61 Bf, Df 60S ribosomal protein L42 4932
39 6T83 76 Z, ob 60S ribosomal protein L42-A 4932
40 6T7T 76 Lo 60S ribosomal protein L42-A 4932
41 6T7I 76 Lo 60S ribosomal protein L42-A 4932
42 6T4Q 75 Lo 60S ribosomal protein L42-A 4932
43 6S47 43 Aq 60S ribosomal protein L42-A 4932
44 6RZZ 37 l 60S ribosomal protein L42-A 4932
45 6S05 37 l 60S ribosomal protein L42-A 4932
46 6RI5 37 l 60S ribosomal protein L42-A 4932
47 6R84 36 C 60S ribosomal protein L42-A 4932
48 6R86 34 C 60S ribosomal protein L42-A 4932
49 6R87 35 C 60S ribosomal protein L42-A 4932
50 6QTZ 37 l 60S ribosomal protein L42-A 4932
51 6QT0 38 l 60S ribosomal protein L42-A 4932
52 6QIK 37 l 60S ribosomal protein L42-A 4932
53 6Q8Y 17 AP 60S ribosomal protein L42-A 4932
54 6N8J 45 q 60S ribosomal protein L42-A 4932
55 6N8K 44 q 60S ribosomal protein L42-A 4932
56 6N8L 44 q 60S ribosomal protein L42-A 4932
57 6N8M 16 Q 60S ribosomal protein L42-A 4932
58 6N8N 19 Q 60S ribosomal protein L42-A 4932
59 6N8O 21 Q 60S ribosomal protein L42-A 4932
60 6I7O 77 AP, XP 60S ribosomal protein L42-A 4932
61 6HD7 6 C 60S ribosomal protein L42-A 4932
62 6GQV 45 o 60S ribosomal protein L42-A 4932
63 6GQ1 45 o 60S ribosomal protein L42-A 4932
64 6GQB 45 o 60S ribosomal protein L42-A 4932
65 5MC6 56 AP 60S ribosomal protein L42-A 4932
66 5H4P 40 o 60S ribosomal protein L42-A 4932
67 5M1J 64 o5 60S ribosomal protein L42-B 4932
68 5T62 43 Q 60S ribosomal protein L42-A 4932
69 5T6R 42 Q 60S ribosomal protein L42-A 4932
70 5JUO 46 TA eL42 (yeast L42) 4932
71 5JUP 46 TA eL42 (yeast L42) 4932
72 5JUS 46 TA eL42 (yeast L42) 4932
73 5JUT 46 TA eL42 (yeast L42) 4932
74 5JUU 46 TA eL42 (yeast L42) 4932
75 5GAK 11 C 60S ribosomal protein L42-A 4932
76 5APN 42 o 60S ribosomal protein L42-A 4932
77 5APO 42 o 60S ribosomal protein L42-A 4932
78 3J77 42 92 60S ribosomal protein L42 4932
79 3J78 42 92 60S ribosomal protein L42 4932
80 3J6X 44 82 60S ribosomal protein L42 4932
81 3J6Y 44 82 60S ribosomal protein L42 4932
82 4V91 43 o EL42 RIBOSOMAL PROTEIN EL42 28985
83 4V8Y 75 Bo 60S RIBOSOMAL PROTEIN L42-A 4932
84 4V8Z 75 Bo 60S RIBOSOMAL PROTEIN L42-A 4932
85 4V8T 41 o 60S RIBOSOMAL PROTEIN L42-A 4932
86 3J0O 24 F Ribosomal protein L36a 9986
87 3J0L 26 F Ribosomal protein L36a 9986
88 4V6I 69 Br 60S ribosomal protein rpL42 (L44e) 4932
89 4V7H 50 BZ 60S ribosomal protein L42 5541
90 4V4B 46 BZ 60S ribosomal protein L42 4932