Structure of PDB 3jb9 Chain A

Receptor sequence

>3jb9A (length=1964) Species: 284812 (Schizosaccharomyces pombe 972h-)

LEKQLNERARKWRASQKSKFGVKRKQGYVQTEKADLPPEHLRKIMKDRGD
MSSRKFRADKRSYLGALKYLPHAVLKLLENMPMPWEEYREVKVLYHVTGA
ITFVNESPRVIEPHFIAQWGTMWMMMRREKRDRKNFKRLRFPPFDDEEPP
FSIDQLLDLEPLEAIRMDLDEEDDAPVMDWFYENKALEDTPHVNGPTYRR
WKLNLPQMANLHRLGYQLLSDLRDDNYFYLFNDNSFFTAKALNVAIPGGP
KFEPLYEFNDIYKLIIRHPIKTEYRIAFPYLYNSRARSVALSEYHQPSNV
FVPPEDPDLPAFFWDPIINPITSRQLTLHELDTSPEDSAIEEDPNFEIPF
DPFFHSEDIEFEHTASALILLWAPHPFNKRSGATKRAQDVPLIKHWYLEH
CPPNQPVKVRVSYQKLLKSHVMNKLHMAHPKSHTNRSLLRQLKNTKFFQS
TSIDWVEAGLQVCRQGYNMLQLLIHRKGLTYLHLDYNCNLKPTKTLTTKE
RKKSRFGNAFHLMREILRLTKLIVDSHVQYRLGNIDAYQLADGLHYIFNH
VGQLTGMYRYKYRLMRQIRACKDFKHLIYYRFNTGPVGKGPGCGFWAPSW
RVWLFFLRGIVPLLERWLGNLLARQFEGRHSTGVAKQITKQRVDSHQDLE
LRAAVMNDILDMIPEGIRQGKSKTILQHLSEAWRCWKANIPWKVPGLPAP
IENMILRYVKSKADWWTSVAHFNRERIRRGATVDKTVAKKNLGRLTRLWL
KAEQERQHNYLKDGPYVTADEAVAIYTTFVHWLESRRFQPIPFPPLSYKH
DTKLLVLALERLKEAYSVKGRLNQSQREELALVEQAYDNPHEMLSQIKRR
LLTMRTFKEVGIEFMDMYSHLIPVYSVDPMEKICDAYLDQYLWFEADRRH
LFPSWVKPSDSEPPPLLVYKWCQGINNLTDVWETSNGECNVLMETRLSKV
FEKVDLTLLNRLMSLLMDTNLASYASAKNNVVLSYKDMSHTNSYGLVRGL
QFSSFIWQFYGLVLDLLILGLQRATEIAGPADAPNDFLHFKDQATETSHP
IRLYTRYIDKVYIMFRFTDEESRDLIQRFLNENPDPTNSNVVNYSKGKKN
CWPRDARMRLMKHDVNLGRAVFWEIRNRLPRSLTTLEWEDTFPSVYSKDN
PNLLFSMTGFEVRILPKIRQNEEFSLKDGVWNLTDNRTKQRTAQAFIRVT
EDGINQFGNRIRQILMSSGSTTFTKIANKWNTALIALMTYYREAAISTPE
LLDLLVKCESKIQTRVKISLNSKMPSRFPPAVFYSPKELGGLGMLSMGHV
LIPQSDLRWSKQTDTGITHFRSGMTTNGEHLIPNLYRYIQPWESEFIDSQ
RVWAEYAMKRQEALQQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYD
KGWRVRTEFKQYQLLKNNPFWWTSQRHDGKLWQLNNYRVDVIQALGGVEG
ILEHTMFKATGFPSWEGLFWEKASGFKKLTNAQRSGLNQIPNRRFTLWWS
PTINRANVYVGFQVQLDLTGIMMHGKIPTLKISLIQIFRSHLWQKIHESV
VWDLCQVLDQELESLQIETVQKETIHPRKSYKMNSSCADILLLAAYKWNV
SRPSLLNDNRDVLDNTTTNKYWIDVQLRFGDYDSHDIERYTRAKFLDYST
DAQSMYPSPTGVLIGIDLCYNMHSAYGNWIPGMKPLIQQSMNKIMKANPA
LYVLRERIRKGLQLYASEQYLSSSNYAELFSNQIQLFVDDTNVYRVTIHK
TFEGNLTTKPINGAIFIFNPRTGQLFLKVIHTSVWAGQKRLGQLAKWKTA
EEVAALIRSLPVEEQPRQIIVTRKGMLDPLEVHLLDFPNITIKGSELQLP
FQAIIKLDKINDLILRATEPQMVLFNLYDDWLQSVSSYTAFSRLILILRA
LNVNTEKTKLILRPDKSIITKENHVWPNLDDQQWLDVEPKLRDLILADYA
KKNNINVASLTNSE

3D structure

• PDB: 3jb9 Structure of a yeast spliceosome at 3.6-angstrom resolution
• Chain: A
• Resolution: 3.6 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	K69 Q76 E78 R155 G241 P242 T243 R245 K286 F298 E299 L301 H432 R443 D446 K451 K475 N480 K481 H483 H486 P487 K488 S489 H490 N492 R497 K618 Y619 R620 R658 F662 R665 G666 P669 V790 D791 K1318	K23 Q30 E32 R109 G195 P196 T197 R199 K240 F252 E253 L255 H375 R386 D389 K394 K418 N423 K424 H426 H429 P430 K431 S432 H433 N435 R440 K561 Y562 R563 R601 F605 R608 G609 P612 V733 D734 K1261
BS02	rna	A	N52 K63 R70 R100 R103 K534 K559 R562 G564 A566 W674 N677 R681 R686 K693 T696 Q698 R699 T1543 N1544	N6 K17 R24 R54 R57 K477 K502 R505 G507 A509 W617 N620 R624 R629 K636 T639 Q641 R642 T1480 N1481
BS03	rna	A	T555 K556 K559	T498 K499 K502
BS04	rna	A	D701 D705 R709 R725 K730 T731 Q734 W740 K797 R801 R804 N880 Q881 R884 K1043 D1044	D644 D648 R652 R668 K673 T674 Q677 W683 K740 R744 R747 N823 Q824 R827 K986 D987

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0004843 cysteine-type deubiquitinase activity
• GO:0008233 peptidase activity
• GO:0008237 metallopeptidase activity
• GO:0017070 U6 snRNA binding
• GO:0030619 U1 snRNA binding
• GO:0030620 U2 snRNA binding
• GO:0030623 U5 snRNA binding
• GO:0097157 pre-mRNA intronic binding

Biological Process

• GO:0000244 spliceosomal tri-snRNP complex assembly
• GO:0000393 spliceosomal conformational changes to generate catalytic conformation
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing

Cellular Component

• GO:0000974 Prp19 complex
• GO:0005634 nucleus
• GO:0005681 spliceosomal complex
• GO:0005682 U5 snRNP
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071013 catalytic step 2 spliceosome
• GO:0071014 post-mRNA release spliceosomal complex

External links

• PDB: RCSB:3jb9, PDBe:3jb9, PDBj:3jb9
• PDBsum: 3jb9
• PubMed: 26292707
• UniProt: O14187|SPP42_SCHPO Pre-mRNA-splicing factor spp42 (Gene Name=spp42)