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 % 62 103 266
95 % 62 107 331
90 % 62 107 350
70 % 63 109 385
50 % 81 157 344
40 % 87 198 263
30 % 87 198 279
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 93 317
95 % 62 95 401
90 % 62 95 420
70 % 63 97 439
50 % 86 183 290
40 % 87 185 293
30 % 87 185 315
Entity #12 | Chains: H
60S ribosomal protein L6-A protein, length: 176 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 97 293
95 % 61 102 358
90 % 61 103 370
70 % 63 106 393
50 % 64 107 447
40 % 65 111 459
30 % 65 111 477
Entity #13 | Chains: I
60S ribosomal protein L7-A protein, length: 244 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 103 270
95 % 62 103 350
90 % 62 103 371
70 % 63 105 398
50 % 86 185 281
40 % 86 185 298
30 % 86 184 323
Entity #14 | Chains: J
60S ribosomal protein L8-A protein, length: 256 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 58 99 321
95 % 65 106 356
90 % 65 106 375
70 % 66 108 401
50 % 87 169 327
40 % 87 171 335
30 % 87 171 354
Entity #15 | Chains: K
60S ribosomal protein L9-A protein, length: 191 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 102 271
95 % 62 102 359
90 % 62 102 377
70 % 63 104 405
50 % 86 193 272
40 % 87 195 274
30 % 155 266 205
Entity #16 | Chains: M
60S ribosomal protein L11-A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 75 490
95 % 62 98 387
90 % 63 100 394
70 % 87 186 259
50 % 89 190 271
40 % 89 190 284
30 % 89 190 300
Entity #17 | Chains: N
60S ribosomal protein L13-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 101 282
95 % 61 101 373
90 % 61 101 393
70 % 62 103 414
50 % 62 103 465
40 % 85 183 305
30 % 85 183 328
Entity #18 | Chains: O
60S ribosomal protein L14-A protein, length: 138 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 103 269
95 % 62 103 357
90 % 62 103 376
70 % 63 105 404
50 % 63 105 459
40 % 63 105 487
30 % 63 105 505
Entity #19 | Chains: Q
60S ribosomal protein L42-A protein, length: 106 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 94 308
95 % 62 94 407
90 % 63 96 411
70 % 85 169 282
50 % 87 181 299
40 % 86 181 308
30 % 87 182 329
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 % 62 94 310
95 % 62 94 405
90 % 62 94 423
70 % 63 96 443
50 % 86 184 283
40 % 87 185 294
30 % 109 208 258
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 % 62 105 262
95 % 64 108 330
90 % 64 108 348
70 % 86 183 266
50 % 88 197 254
40 % 88 197 268
30 % 88 197 283
Entity #23 | Chains: b
60S ribosomal protein L16-A protein, length: 199 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 307
95 % 56 95 403
90 % 62 102 380
70 % 63 104 407
50 % 63 105 458
40 % 63 106 484
30 % 63 106 502
Entity #24 | Chains: c
60S ribosomal protein L17-A protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 106 257
95 % 61 106 334
90 % 62 108 342
70 % 62 108 389
50 % 86 195 259
40 % 86 195 272
30 % 86 195 288
Entity #25 | Chains: d
60S ribosomal protein L18-A protein, length: 186 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 103 268
95 % 62 103 355
90 % 63 105 363
70 % 63 105 403
50 % 85 186 287
40 % 85 191 289
30 % 85 191 311
Entity #26 | Chains: e
60S ribosomal protein L19-A protein, length: 189 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 59 97 297
95 % 59 97 391
90 % 59 97 408
70 % 60 100 421
50 % 85 185 285
40 % 85 186 296
30 % 85 186 320
Entity #27 | Chains: f
60S ribosomal protein L20-A protein, length: 172 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 101 283
95 % 61 101 377
90 % 62 103 383
70 % 62 103 416
50 % 84 176 318
40 % 85 177 324
30 % 85 178 337
Entity #28 | Chains: g
60S ribosomal protein L21-A protein, length: 160 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 97 294
95 % 62 97 390
90 % 63 99 400
70 % 63 99 428
50 % 85 175 316
40 % 85 181 317
30 % 87 188 309
Entity #29 | Chains: h
60S ribosomal protein L22-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 42 72 464
95 % 42 72 606
90 % 42 72 635
70 % 43 73 657
50 % 43 73 685
40 % 43 73 723
30 % 44 74 722
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 % 62 104 265
95 % 62 104 348
90 % 63 106 353
70 % 87 197 240
50 % 87 198 252
40 % 87 198 262
30 % 87 198 277
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 64 483
95 % 43 66 629
90 % 43 66 660
70 % 44 67 678
50 % 44 67 716
40 % 53 114 491
30 % 53 114 512
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 43 77 434
95 % 43 77 560
90 % 44 78 581
70 % 44 78 601
50 % 44 78 635
40 % 44 80 660
30 % 44 81 671
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 108 250
95 % 62 108 322
90 % 63 110 334
70 % 63 110 382
50 % 87 193 265
40 % 87 193 279
30 % 87 193 293
Entity #34 | Chains: m
60S ribosomal protein L27-A protein, length: 136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 97 304
95 % 61 97 396
90 % 62 99 404
70 % 62 99 436
50 % 84 171 325
40 % 85 184 299
30 % 86 186 316
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 95 309
95 % 62 98 383
90 % 63 100 391
70 % 63 100 420
50 % 86 188 275
40 % 87 189 288
30 % 87 191 299
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 89 330
95 % 61 89 434
90 % 62 91 444
70 % 62 91 472
50 % 62 91 508
40 % 62 91 548
30 % 62 91 576
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 64 103 263
95 % 64 103 346
90 % 65 105 352
70 % 65 105 395
50 % 79 146 361
40 % 79 146 375
30 % 79 146 391
Entity #38 | Chains: q
60S ribosomal protein L31-A protein, length: 113 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 101 275
95 % 62 101 369
90 % 62 101 388
70 % 63 103 410
50 % 86 185 282
40 % 86 185 295
30 % 86 185 319
Entity #39 | Chains: r
60S ribosomal protein L32 protein, length: 130 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 104 264
95 % 62 104 347
90 % 62 104 368
70 % 63 106 396
50 % 87 189 274
40 % 87 193 280
30 % 87 194 290
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 20761
95 % 4 5 18730
90 % 4 5 18387
70 % 4 5 17076
50 % 4 5 15375
40 % 4 5 14268
30 % 4 5 12984
Entity #40 | Chains: s
60S ribosomal protein L33-A protein, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 102 274
95 % 61 102 366
90 % 61 102 384
70 % 62 104 411
50 % 84 181 307
40 % 85 183 313
30 % 85 183 334
Entity #41 | Chains: t
60S ribosomal protein L34-A protein, length: 121 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 97 300
95 % 61 97 393
90 % 61 97 410
70 % 62 99 430
50 % 84 170 326
40 % 84 170 338
30 % 84 170 358
Entity #42 | Chains: u
60S ribosomal protein L35-A protein, length: 120 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 107 253
95 % 62 107 328
90 % 62 107 346
70 % 63 109 384
50 % 86 188 280
40 % 87 199 259
30 % 88 201 270
Entity #43 | Chains: v
60S ribosomal protein L36-A protein, length: 100 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 98 299
95 % 61 102 370
90 % 61 102 389
70 % 62 104 413
50 % 62 104 463
40 % 85 178 320
30 % 85 188 312
Entity #44 | Chains: w
60S ribosomal protein L37-A protein, length: 88 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 104 261
95 % 62 104 345
90 % 62 104 366
70 % 72 148 309
50 % 86 193 266
40 % 86 193 282
30 % 86 193 295
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 61 97 305
95 % 61 97 399
90 % 61 97 416
70 % 62 99 438
50 % 62 99 486
40 % 63 106 474
30 % 63 106 495
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 63 101 277
95 % 63 101 368
90 % 63 101 386
70 % 85 177 275
50 % 86 189 273
40 % 86 191 283
30 % 87 192 297
Entity #47 | Chains: z
Ubiquitin-60S ribosomal protein L40 protein, length: 128 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 35 1346
95 % 14 36 1736
90 % 18 62 992
70 % 18 65 967
50 % 18 65 999
40 % 18 65 1030
30 % 18 65 1082
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 29338
95 % 3 4 24110
90 % 3 4 19923
70 % 3 4 20922
50 % 15 66 1128
40 % 15 66 1169
30 % 15 66 1215
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 1880
95 % 15 31 2400
90 % 15 31 2459
70 % 16 32 2421
50 % 18 36 1956
40 % 18 36 2000
30 % 19 38 1896
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 13966
95 % 6 7 13463
90 % 6 8 11535
70 % 6 8 11037
50 % 6 8 10207
40 % 6 8 9698
30 % 6 8 9016
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 7670
95 % 9 11 8421
90 % 9 11 8372
70 % 9 11 8189
50 % 9 11 7699
40 % 9 11 7409
30 % 9 11 6981
Entity #8 | Chains: D
60S ribosomal protein L2-A protein, length: 254 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 62 97 295
95 % 62 97 388
90 % 63 99 396
70 % 85 174 280
50 % 86 187 277
40 % 154 258 200
30 % 154 258 212
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 60 101 289
95 % 62 103 354
90 % 63 105 361
70 % 63 105 400
50 % 88 198 251
40 % 88 198 261
30 % 88 200 271

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 6TNU 80 AP 60S ribosomal protein L42-A 4932
40 6TB3 80 AP 60S ribosomal protein L42-A 4932
41 6T83 76 Z, ob 60S ribosomal protein L42-A 4932
42 6T7T 76 Lo 60S ribosomal protein L42-A 4932
43 6T7I 76 Lo 60S ribosomal protein L42-A 4932
44 6T4Q 75 Lo 60S ribosomal protein L42-A 4932
45 6SV4 77 AP, XP, zP 60S ribosomal protein L42-A 4932
46 6SNT 76 ab 60S ribosomal protein L42-A 4932
47 6S47 43 Aq 60S ribosomal protein L42-A 4932
48 6RZZ 37 l 60S ribosomal protein L42-A 4932
49 6S05 37 l 60S ribosomal protein L42-A 4932
50 6RI5 37 l 60S ribosomal protein L42-A 4932
51 6R84 36 C 60S ribosomal protein L42-A 4932
52 6R86 34 C 60S ribosomal protein L42-A 4932
53 6R87 35 C 60S ribosomal protein L42-A 4932
54 6QTZ 37 l 60S ribosomal protein L42-A 4932
55 6QT0 38 l 60S ribosomal protein L42-A 4932
56 6QIK 37 l 60S ribosomal protein L42-A 4932
57 6Q8Y 17 AP 60S ribosomal protein L42-A 4932
58 6N8J 45 q 60S ribosomal protein L42-A 4932
59 6N8K 44 q 60S ribosomal protein L42-A 4932
60 6N8L 44 q 60S ribosomal protein L42-A 4932
61 6N8M 16 Q 60S ribosomal protein L42-A 4932
62 6N8N 19 Q 60S ribosomal protein L42-A 4932
63 6N8O 21 Q 60S ribosomal protein L42-A 4932
64 6I7O 77 AP, XP 60S ribosomal protein L42-A 4932
65 6HD7 6 C 60S ribosomal protein L42-A 4932
66 6GQV 45 o 60S ribosomal protein L42-A 4932
67 6GQ1 45 o 60S ribosomal protein L42-A 4932
68 6GQB 45 o 60S ribosomal protein L42-A 4932
69 5MC6 56 AP 60S ribosomal protein L42-A 4932
70 5H4P 40 o 60S ribosomal protein L42-A 4932
71 5M1J 64 o5 60S ribosomal protein L42-B 4932
72 5T62 43 Q 60S ribosomal protein L42-A 4932
73 5T6R 42 Q 60S ribosomal protein L42-A 4932
74 5JUO 46 TA eL42 (yeast L42) 4932
75 5JUP 46 TA eL42 (yeast L42) 4932
76 5JUS 46 TA eL42 (yeast L42) 4932
77 5JUT 46 TA eL42 (yeast L42) 4932
78 5JUU 46 TA eL42 (yeast L42) 4932
79 5GAK 11 C 60S ribosomal protein L42-A 4932
80 5APN 42 o 60S ribosomal protein L42-A 4932
81 5APO 42 o 60S ribosomal protein L42-A 4932
82 3J77 42 92 60S ribosomal protein L42 4932
83 3J78 42 92 60S ribosomal protein L42 4932
84 3J6X 44 82 60S ribosomal protein L42 4932
85 3J6Y 44 82 60S ribosomal protein L42 4932
86 4V91 43 o EL42 RIBOSOMAL PROTEIN EL42 28985
87 4V8Y 75 Bo 60S RIBOSOMAL PROTEIN L42-A 4932
88 4V8Z 75 Bo 60S RIBOSOMAL PROTEIN L42-A 4932
89 4V8T 41 o 60S RIBOSOMAL PROTEIN L42-A 4932
90 3J0O 24 F Ribosomal protein L36a 9986
91 3J0L 26 F Ribosomal protein L36a 9986
92 4V6I 69 Br 60S ribosomal protein rpL42 (L44e) 4932
93 4V7H 50 BZ 60S ribosomal protein L42 5541
94 4V4B 46 BZ 60S ribosomal protein L42 4932