Structure of PDB 3jb9 Chain A Binding Site BS04

Receptor Information

>3jb9 Chain A (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

Ligand information

>3jb9 Chain P (length=111)

auucucucuuugccuuuuggcuuagaucaaguguaguaucuguaucuugu
uuuugguuuuuggaaagccucugggcuaugcuuuccucuugcuauugcac
uacuggcaagc

..................................................
.............<<<<<.<.......>.>>>>>...<<<<<<.......
....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3jb9 Structure of a yeast spliceosome at 3.6-angstrom resolution
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): D701 D705 R709 R725 K730 T731 Q734 W740 K797 R801 R804 N880 Q881 R884 K1043 D1044
• Binding residue (residue number reindexed from 1): 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)