5XJC

Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom


Sequence Similarity Clusters for the Entities in PDB 5XJC

Entity #1 | Chains: A
Pre-mRNA-processing-splicing factor 8 protein, length: 2335 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 16 18 3778
95 % 16 18 4400
90 % 16 18 4559
70 % 16 19 4221
50 % 26 41 1745
40 % 26 41 1795
30 % 26 41 1818
Entity #10 | Chains: J
Crooked neck-like protein 1 protein, length: 848 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 12 5952
95 % 11 12 6915
90 % 11 12 6906
70 % 11 12 6811
50 % 11 12 6471
40 % 11 12 6276
30 % 11 12 5937
Entity #11 | Chains: K
Pre-mRNA-splicing factor SPF27 protein, length: 225 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 10 8373
95 % 9 10 8755
90 % 9 10 8691
70 % 9 10 8458
50 % 9 10 7890
40 % 9 10 7613
30 % 9 10 7114
Entity #12 | Chains: L
Cell division cycle 5-like protein protein, length: 802 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 12 6390
95 % 11 12 7571
90 % 11 12 7546
70 % 11 12 7387
50 % 11 12 6954
40 % 11 12 6724
30 % 11 12 6318
Entity #13 | Chains: M
Pre-mRNA-splicing factor SYF2 protein, length: 243 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 5 6 15105
95 % 5 6 14533
90 % 5 6 14277
70 % 5 6 13493
50 % 5 6 12278
40 % 5 6 11494
30 % 5 6 10563
Entity #14 | Chains: N
Protein BUD31 homolog protein, length: 144 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 10 11 7349
95 % 10 11 7857
90 % 10 11 7819
70 % 10 11 7624
50 % 18 29 2574
40 % 18 29 2606
30 % 18 29 2581
Entity #15 | Chains: O
Pre-mRNA-splicing factor RBM22 protein, length: 420 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 10 7559
95 % 9 10 8514
90 % 9 10 8455
70 % 9 10 8220
50 % 9 10 7709
40 % 9 10 7436
30 % 9 10 6965
Entity #16 | Chains: P
Spliceosome-associated protein CWC15 homolog protein, length: 229 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 12 6662
95 % 11 12 6702
90 % 11 12 6711
70 % 11 12 6605
50 % 11 12 6482
40 % 11 12 6136
30 % 11 12 5952
Entity #17 | Chains: Q
Intron-binding protein aquarius protein, length: 1485 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 10 11 7121
95 % 10 11 7834
90 % 10 11 7792
70 % 10 11 7598
50 % 10 11 7144
40 % 10 11 6906
30 % 10 11 6476
Entity #18 | Chains: R
SNW domain-containing protein 1 protein, length: 536 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 7 8 11265
95 % 10 11 7785
90 % 10 11 7737
70 % 10 11 7550
50 % 10 11 7105
40 % 10 12 6193
30 % 10 12 6201
Entity #19 | Chains: S
Peptidyl-prolyl cis-trans isomerase-like 1 protein, length: 166 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 13 5678
95 % 11 13 6478
90 % 11 13 6494
70 % 11 13 6400
50 % 11 13 6110
40 % 11 13 5950
30 % 11 13 5679
Entity #2 | Chains: B
U5 snRNA rna, length: 117 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #20 | Chains: T
Pleiotropic regulator 1 protein, length: 514 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 10 10 8196
95 % 10 11 7772
90 % 10 11 7736
70 % 10 11 7549
50 % 10 11 7104
40 % 10 11 6860
30 % 10 11 6432
Entity #21 | Chains: U
Serine/arginine repetitive matrix protein 2 protein, length: 2752 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 7 8 9996
95 % 7 8 10778
90 % 7 8 10664
70 % 7 8 10232
50 % 7 8 9524
40 % 7 8 9081
30 % 7 8 8440
Entity #22 | Chains: V
Pre-mRNA-splicing factor CWC22 homolog protein, length: 908 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 8 9 9003
95 % 8 9 9882
90 % 8 9 9800
70 % 8 9 9506
50 % 8 9 8851
40 % 8 9 8476
30 % 8 9 7902
Entity #23 | Chains: W
Pre-mRNA-processing factor 17 protein, length: 579 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 10 8304
95 % 9 10 9100
90 % 9 10 8542
70 % 9 10 8309
50 % 9 10 8165
40 % 10 12 6314
30 % 10 12 5970
Entity #24 | Chains: X
PRKR-interacting protein 1 protein, length: 184 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 2 2 52635
95 % 2 2 34164
90 % 2 2 34571
70 % 2 2 30815
50 % 2 2 26919
40 % 2 2 24563
30 % 2 2 21853
Entity #25 | Chains: Y
ATP-dependent RNA helicase DHX8 protein, length: 1220 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 1 71428
95 % 3 4 19148
90 % 3 4 18768
70 % 3 4 20804
50 % 3 4 18405
40 % 3 4 16929
30 % 3 4 15245
Entity #26 | Chains: Z
Pre-mRNA-splicing factor SLU7 protein, length: 586 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 3 31216
95 % 3 3 29354
90 % 3 3 26169
70 % 3 3 23825
50 % 3 3 20906
40 % 3 3 19147
30 % 3 3 17179
Entity #27 | Chains: a,h
Small nuclear ribonucleoprotein Sm D3 protein, length: 126 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 17 19 867
95 % 17 20 1107
90 % 17 20 1136
70 % 17 20 1161
50 % 17 20 1194
40 % 17 20 1234
30 % 17 20 1270
Entity #28 | Chains: b,i
Small nuclear ribonucleoprotein-associated proteins B and B' protein, length: 231 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 15 17 1315
95 % 15 17 1728
90 % 15 17 1767
70 % 15 17 1809
50 % 15 17 1847
40 % 15 17 1876
30 % 15 17 1917
Entity #29 | Chains: c,j
Small nuclear ribonucleoprotein Sm D1 protein, length: 119 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 20 23 551
95 % 20 23 745
90 % 20 23 776
70 % 20 24 776
50 % 20 24 821
40 % 20 24 859
30 % 20 24 894
Entity #3 | Chains: C
116 kDa U5 small nuclear ribonucleoprotein component protein, length: 972 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 15 4735
95 % 16 18 4338
90 % 16 18 4414
70 % 16 18 4400
50 % 16 19 4052
40 % 16 19 3999
30 % 26 41 1791
Entity #30 | Chains: d,k
Small nuclear ribonucleoprotein Sm D2 protein, length: 118 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 25 28 479
95 % 27 30 637
90 % 27 30 664
70 % 27 30 692
50 % 42 58 445
40 % 42 58 466
30 % 42 58 486
Entity #31 | Chains: f,m
Small nuclear ribonucleoprotein F protein, length: 86 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 24 27 501
95 % 24 27 685
90 % 24 27 715
70 % 24 27 751
50 % 24 27 793
40 % 24 27 829
30 % 24 27 869
Entity #32 | Chains: e,l
Small nuclear ribonucleoprotein E protein, length: 92 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 25 28 483
95 % 25 28 661
90 % 25 28 692
70 % 25 28 719
50 % 25 28 754
40 % 25 28 787
30 % 25 28 833
Entity #33 | Chains: g,n
Small nuclear ribonucleoprotein G protein, length: 76 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 25 28 477
95 % 25 28 649
90 % 25 28 680
70 % 25 28 709
50 % 40 56 455
40 % 40 57 474
30 % 40 57 494
Entity #34 | Chains: o
U2 small nuclear ribonucleoprotein A' protein, length: 255 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 11 7468
95 % 13 14 6037
90 % 13 14 6191
70 % 13 14 5906
50 % 13 14 5661
40 % 13 14 5506
30 % 13 14 5258
Entity #35 | Chains: p
U2 small nuclear ribonucleoprotein B'' protein, length: 225 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 13 14 5005
95 % 13 14 5888
90 % 13 14 5936
70 % 13 14 5933
50 % 13 14 5612
40 % 13 14 5529
30 % 13 14 5211
Entity #36 | Chains: q,r,s,t
Pre-mRNA-processing factor 19 protein, length: 504 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 10 1252
95 % 9 10 1693
90 % 9 10 1677
70 % 9 10 1758
50 % 9 10 1797
40 % 9 10 1847
30 % 9 11 1674
Entity #37 | Chains: u
Eukaryotic initiation factor 4A-III protein, length: 411 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 11 12 3428
95 % 13 14 3682
90 % 13 14 3689
70 % 16 17 2625
50 % 19 20 2137
40 % 30 31 1540
30 % 38 39 1238
Entity #38 | Chains: v
Protein mago nashi homolog 2 protein, length: 148 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 10 10 4621
95 % 10 10 5339
90 % 14 14 3772
70 % 14 14 3690
50 % 14 14 3628
40 % 14 14 3618
30 % 14 14 3529
Entity #39 | Chains: w
RNA-binding protein 8A protein, length: 174 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 3 32409
95 % 3 3 28816
90 % 3 3 27756
70 % 3 3 25138
50 % 6 6 10055
40 % 6 6 9523
30 % 6 6 8819
Entity #4 | Chains: D
U5 small nuclear ribonucleoprotein 200 kDa helicase protein, length: 2136 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 12 13 5578
95 % 12 13 6282
90 % 12 13 6302
70 % 12 13 6209
50 % 12 13 5930
40 % 16 25 2915
30 % 16 25 2873
Entity #40 | Chains: x
Protein CASC3 protein, length: 703 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 3 3 35425
95 % 3 3 28505
90 % 3 3 27453
70 % 3 3 24880
50 % 3 3 21860
40 % 3 3 19989
30 % 3 3 17906
Entity #5 | Chains: E
U5 small nuclear ribonucleoprotein 40 kDa protein protein, length: 357 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 14 16 4255
95 % 14 16 5084
90 % 14 16 5150
70 % 14 16 5317
50 % 14 16 4798
40 % 14 16 5000
30 % 14 16 4792
Entity #6 | Chains: F
U6 snRNA rna, length: 107 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #7 | Chains: G
pre-mRNA rna, length: 275 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #8 | Chains: H
Homo sapiens small nuclear RNA (U2) gene rna, length: 188 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
Entity #9 | Chains: I
Pre-mRNA-splicing factor SYF1 protein, length: 855 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 9 10 8303
95 % 9 10 8598
90 % 9 10 8541
70 % 9 10 8308
50 % 9 10 7780
40 % 9 10 7502
30 % 9 10 7024

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