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 95 264
95 % 54 99 332
90 % 54 99 341
70 % 54 100 381
50 % 71 147 340
40 % 72 183 263
30 % 72 183 281
Entity #11 | Chains: G
60S ribosomal protein L5 protein, length: 297 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 85 311
95 % 54 87 404
90 % 54 87 421
70 % 54 88 452
50 % 71 168 292
40 % 72 170 299
30 % 72 170 320
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 95 265
95 % 54 95 357
90 % 54 96 362
70 % 54 97 393
50 % 55 98 450
40 % 56 102 462
30 % 56 102 476
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 95 263
95 % 54 95 356
90 % 54 95 369
70 % 54 97 391
50 % 71 171 282
40 % 71 171 298
30 % 71 170 324
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 91 312
95 % 57 98 353
90 % 57 98 370
70 % 57 99 395
50 % 74 156 331
40 % 74 158 343
30 % 74 158 357
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 94 269
95 % 54 94 360
90 % 54 94 372
70 % 54 95 403
50 % 71 178 267
40 % 139 250 196
30 % 428 719 25
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 67 498
95 % 54 90 381
90 % 54 91 390
70 % 72 171 255
50 % 74 175 265
40 % 74 175 286
30 % 74 175 305
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 93 280
95 % 53 93 371
90 % 53 93 385
70 % 53 94 414
50 % 53 94 466
40 % 70 168 310
30 % 70 168 330
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 95 267
95 % 54 95 355
90 % 54 95 367
70 % 54 96 397
50 % 54 96 460
40 % 54 96 487
30 % 54 96 514
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 86 304
95 % 54 86 407
90 % 54 87 420
70 % 70 157 280
50 % 72 169 289
40 % 71 169 303
30 % 72 170 322
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 86 307
95 % 54 86 406
90 % 54 86 424
70 % 54 87 457
50 % 71 169 286
40 % 72 170 302
30 % 94 193 254
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 97 258
95 % 55 99 334
90 % 55 99 346
70 % 71 168 263
50 % 73 182 252
40 % 73 182 267
30 % 73 182 287
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 87 301
95 % 48 87 403
90 % 54 94 371
70 % 54 95 402
50 % 71 170 283
40 % 71 171 294
30 % 71 171 317
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 98 247
95 % 53 98 336
90 % 53 99 342
70 % 53 99 382
50 % 71 180 254
40 % 71 180 275
30 % 71 180 294
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 95 261
95 % 54 95 354
90 % 54 96 356
70 % 54 96 396
50 % 70 169 297
40 % 70 176 292
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 89 284
95 % 51 89 384
90 % 51 89 397
70 % 51 91 423
50 % 69 169 290
40 % 69 170 304
30 % 69 170 325
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 93 278
95 % 53 93 375
90 % 53 94 382
70 % 53 94 417
50 % 69 161 322
40 % 70 162 329
30 % 70 163 341
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 89 286
95 % 54 89 390
90 % 54 90 393
70 % 54 90 431
50 % 70 160 319
40 % 70 166 321
30 % 72 173 314
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 68 438
95 % 38 68 596
90 % 38 68 614
70 % 38 68 667
50 % 38 68 699
40 % 38 68 722
30 % 39 69 732
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 96 254
95 % 54 96 352
90 % 54 97 355
70 % 72 182 236
50 % 139 253 179
40 % 139 253 194
30 % 139 253 203
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 63 443
95 % 40 63 603
90 % 40 63 631
70 % 40 63 673
50 % 40 63 705
40 % 44 105 491
30 % 44 105 520
Entity #32 | Chains: k
60S ribosomal protein L25 protein, length: 142 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 39 73 413
95 % 39 73 539
90 % 39 73 567
70 % 39 73 599
50 % 39 73 641
40 % 39 75 662
30 % 39 76 690
Entity #33 | Chains: l
60S ribosomal protein L26-A protein, length: 127 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 100 242
95 % 54 100 327
90 % 54 101 334
70 % 54 101 375
50 % 71 177 261
40 % 71 177 283
30 % 71 177 302
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 89 395
90 % 53 90 404
70 % 53 90 441
50 % 69 156 332
40 % 70 169 306
30 % 71 171 323
Entity #35 | Chains: n
60S ribosomal protein L28 protein, length: 149 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 87 305
95 % 54 90 380
90 % 54 91 388
70 % 54 91 422
50 % 71 173 276
40 % 72 174 290
30 % 72 176 304
Entity #36 | Chains: o
60S ribosomal protein L29 protein, length: 59 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 81 323
95 % 53 81 428
90 % 53 82 445
70 % 53 82 479
50 % 53 82 516
40 % 53 82 550
30 % 53 82 572
Entity #37 | Chains: p
60S ribosomal protein L30 protein, length: 105 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 56 95 256
95 % 56 95 349
90 % 56 96 353
70 % 56 96 394
50 % 69 136 360
40 % 69 136 380
30 % 69 136 388
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 93 274
95 % 54 93 367
90 % 54 93 378
70 % 54 94 404
50 % 71 170 285
40 % 71 170 300
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 96 255
95 % 54 96 347
90 % 54 96 361
70 % 54 97 392
50 % 72 174 270
40 % 72 178 279
30 % 72 179 296
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 18569
95 % 4 5 17982
90 % 4 5 17653
70 % 4 5 15873
50 % 4 5 14846
40 % 4 5 13780
30 % 4 5 12153
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 94 272
95 % 53 94 366
90 % 53 94 377
70 % 53 95 411
50 % 69 166 308
40 % 70 168 318
30 % 70 168 336
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 89 398
90 % 53 89 414
70 % 53 90 445
50 % 69 155 336
40 % 69 155 351
30 % 69 155 365
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 99 244
95 % 54 99 331
90 % 54 99 339
70 % 54 100 378
50 % 70 172 287
40 % 71 183 261
30 % 72 185 274
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 90 287
95 % 53 94 368
90 % 53 94 379
70 % 53 95 408
50 % 53 95 462
40 % 70 163 326
30 % 70 173 315
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 96 257
95 % 54 96 351
90 % 54 96 366
70 % 58 132 317
50 % 71 178 260
40 % 71 178 281
30 % 71 178 299
Entity #45 | Chains: x
60S ribosomal protein L38 protein, length: 78 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 53 89 296
95 % 53 89 394
90 % 53 89 409
70 % 53 90 439
50 % 53 90 483
40 % 54 97 482
30 % 54 97 505
Entity #46 | Chains: y
60S ribosomal protein L39 protein, length: 51 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 54 92 276
95 % 54 92 373
90 % 54 92 384
70 % 70 162 270
50 % 71 174 271
40 % 71 176 285
30 % 72 177 301
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 1566
95 % 9 31 2082
90 % 10 54 1132
70 % 10 57 1084
50 % 10 57 1121
40 % 10 57 1154
30 % 10 57 1199
Entity #48 | Chains: L
Ribosomal protein L12 protein, length: 165 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 4 27586
95 % 3 4 22644
90 % 3 4 21532
70 % 3 4 19769
50 % 13 64 1072
40 % 13 64 1108
30 % 13 64 1149
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 1728
95 % 15 31 2282
90 % 15 31 2330
70 % 16 32 2353
50 % 18 36 1845
40 % 18 36 1892
30 % 19 38 1763
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 12684
95 % 6 7 12984
90 % 6 8 11234
70 % 6 8 10781
50 % 6 8 9910
40 % 6 8 9414
30 % 6 8 8736
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 7088
95 % 9 11 7793
90 % 9 11 7774
70 % 9 11 7582
50 % 9 11 7134
40 % 9 11 6907
30 % 9 11 6492
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 89 289
95 % 54 89 392
90 % 54 90 395
70 % 70 159 276
50 % 71 172 277
40 % 139 243 201
30 % 139 243 211
Entity #9 | Chains: E
60S ribosomal protein L3 protein, length: 387 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 52 93 282
95 % 54 95 358
90 % 54 96 363
70 % 54 96 400
50 % 73 183 245
40 % 73 183 258
30 % 73 185 273

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 4U4O 40 L3, l3 60S ribosomal protein L3 4932
29 5DGV 40 L3, l3 60S ribosomal protein L3 4932
30 5DGE 40 L3, l3 60S ribosomal protein L3 4932
31 5NDW 28 L3, l3 60S ribosomal protein L3 4932
32 5NDG 40 L3, l3 60S ribosomal protein L3 4932
33 5DC3 40 L3, l3 60S ribosomal protein L3 4932
34 5DGF 40 L3, l3 60S ribosomal protein L3 4932
35 5TGM 40 L3, l3 60S ribosomal protein L3 4932
36 4V7R 34 BC, DC 60S ribosomal protein L3 4932
37 6S47 5 AE 60S ribosomal protein L3 4932
38 6RZZ 3 C 60S ribosomal protein L3 4932
39 6S05 3 C 60S ribosomal protein L3 4932
40 6RI5 3 C 60S ribosomal protein L3 4932
41 6R84 42 F 60S ribosomal protein L3 4932
42 6R86 40 F 60S ribosomal protein L3 4932
43 6R87 41 F 60S ribosomal protein L3 4932
44 6QTZ 3 C 60S ribosomal protein L3 4932
45 6QT0 3 C 60S ribosomal protein L3 4932
46 6QIK 3 C 60S ribosomal protein L3 4932
47 6Q8Y 38 BA 60S ribosomal protein L3 4932
48 6N8J 5 B 60S ribosomal protein L3 4932
49 6N8K 5 B 60S ribosomal protein L3 4932
50 6N8L 5 B 60S ribosomal protein L3 4932
51 6N8M 6 E 60S ribosomal protein L3 4932
52 6N8N 9 E 60S ribosomal protein L3 4932
53 6N8O 10 E 60S ribosomal protein L3 4932
54 6I7O 5 BA, YA 60S ribosomal protein L3 4932
55 6HD7 9 F 60S ribosomal protein L3 4932
56 6GQV 7 B 60S ribosomal protein L3 4932
57 6GQ1 7 B 60S ribosomal protein L3 4932
58 6GQB 7 B 60S ribosomal protein L3 4932
59 6FT6 3 B 60S ribosomal protein L3 4932
60 5Z3G 6 F 60S ribosomal protein L3 4932
61 6C0F 5 B 60S ribosomal protein L3 4932
62 6EM1 16 B 60S ribosomal protein L3 4932
63 6EM4 11 B 60S ribosomal protein L3 Backbone model 4932
64 6EM5 27 B 60S ribosomal protein L3 Backbone model 4932
65 6ELZ 28 B 60S ribosomal protein L3 4932
66 5MC6 67 BA 60S ribosomal protein L3 4932
67 5H4P 5 B 60S ribosomal protein L3 4932
68 5M1J 42 B5 60S ribosomal protein L3 4932
69 5T62 6 E 60S ribosomal protein L3 4932
70 5T6R 5 E 60S ribosomal protein L3 4932
71 5JUO 7 G uL3 (yeast L3) 4932
72 5JUP 7 G uL3 (yeast L3) 4932
73 5JUS 7 G uL3 (yeast L3) 4932
74 5JUT 7 G uL3 (yeast L3) 4932
75 5JUU 7 G uL3 (yeast L3) 4932
76 5JCS 3 B 60S ribosomal protein L3 4932
77 3JCT 2 B 60S ribosomal protein L3 4932
78 5GAK 17 F 60S ribosomal protein L3 4932
79 5FL8 2 B 60S ribosomal protein L3 4932
80 5APN 5 B 60S ribosomal protein L3 4932
81 5APO 5 B 60S ribosomal protein L3 4932
82 3J77 3 L3 60S ribosomal protein L3 4932
83 3J78 3 L3 60S ribosomal protein L3 4932
84 3J6X 6 L3 60S ribosomal protein L3 4932
85 3J6Y 6 L3 60S ribosomal protein L3 4932
86 4V91 5 B UL3 RIBOSOMAL PROTEIN UL3 28985
87 4V7F 6 C 60S ribosomal protein L3 4932
88 4V8Y 36 BB 60S RIBOSOMAL PROTEIN L3 4932
89 4V8Z 36 BB 60S RIBOSOMAL PROTEIN L3 4932
90 4V8T 2 B 60S RIBOSOMAL PROTEIN L3 4932
91 4V6I 32 BC 60S ribosomal protein rpL3 (L3p) 4932
92 4V7H 27 BC 60S ribosomal protein L3 5541
93 4V4B 22 BC 60S ribosomal protein L3 4932