Structure of PDB 8r0a Chain A Binding Site BS03

Receptor Information

>8r0a Chain A (length=2210) Species: 9606 (Homo sapiens)

AQKEDMPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLEN
MPMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREK
RDRRHFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLD
WFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYF
YLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIR
QPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPL
INPISHRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALL
WAPRPFNLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYV
LNALKHRPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLN
LLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTK
LVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMC
KDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNL
LARQFQRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRC
WKANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDK
TVCKKNLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLES
RRFSPIPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQ
AYDNPHEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITD
AYLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETS
EGECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINY
KDMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPN
DFLSFQDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPD
PNNENIVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQ
WENSFVSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNE
VTKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIG
LMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTP
KELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLY
RYIQPWESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRI
NTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNN
YRTDMIQALGGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLT
NAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTL
KISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKS
YKMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWG
DYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWF
PGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYG
ELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFL
KIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGML
DPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNL
YDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWP
TLTDEEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEIFSS
KTEWRVRAISAANLHLRTNHIYVSSDDIKETYTYILPKNVLKKFICISDL
RAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLK
EMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTP
GSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGF
FMVPAQSSWNYNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALV
YSADREDLYA

Ligand information

>8r0a Chain z (length=11)

aagguaaguau

...........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8r0a Structural insights into the cross-exon to cross-intron spliceosome switch
• Resolution: 5.8 Å
• Binding residue (original residue number in PDB): F540 S1305 F1551 G1564 K1565
• Binding residue (residue number reindexed from 1): F485 S1236 F1482 G1495 K1496

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0008233 peptidase activity
• GO:0017070 U6 snRNA binding
• GO:0030619 U1 snRNA binding
• GO:0030620 U2 snRNA binding
• GO:0030623 U5 snRNA binding
• GO:0070530 K63-linked polyubiquitin modification-dependent protein binding
• GO:0097157 pre-mRNA intronic binding
• GO:0140492 metal-dependent deubiquitinase activity

Biological Process

• GO:0000244 spliceosomal tri-snRNP complex assembly
• GO:0000375 RNA splicing, via transesterification reactions
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing
• GO:0071222 cellular response to lipopolysaccharide
• GO:0071356 cellular response to tumor necrosis factor

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005682 U5 snRNP
• GO:0016020 membrane
• GO:0016607 nuclear speck
• GO:0030532 small nuclear ribonucleoprotein complex
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071006 U2-type catalytic step 1 spliceosome
• GO:0071007 U2-type catalytic step 2 spliceosome
• GO:0071013 catalytic step 2 spliceosome

External links

• PDB: RCSB:8r0a, PDBe:8r0a, PDBj:8r0a
• PDBsum: 8r0a
• PubMed: 38778104
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)