Structure of PDB 8i0p Chain A Binding Site BS05

Receptor Information

>8i0p Chain A (length=2149) Species: 9606 (Homo sapiens)

QKEDMPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENM
PMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKR
DRRHFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLDW
FYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYFY
LFDLKAFFTSKALNMAIPGGPKFEPLVRDINKIIIRQPIRTEYKIAFPYL
YNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQE
PLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTR
RALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKK
RYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLD
YNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNV
DAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTG
PVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKVTK
QRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANI
PWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKK
NLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSP
IPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNP
HEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQ
YLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECN
VMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNH
TNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSF
QDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNEN
IVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSF
VSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKER
TAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYF
REAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGG
LGMLSMGHVLRSGMSHEEDQLIPNLYRYIQPWESEFIDSQRVWAEYALKR
QEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTDFK
QYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGT
YFPTWEGLFWEKNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHG
KIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETI
HPRKSYKMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDI
QLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSA
YGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYSSEPTQIIWF
VDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAG
QKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDF
PNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISS
YTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKV
EVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEWRVRAISAANLHLR
TNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPDN
PQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWIHTQPNESP
QLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAYKLTPSGYE
WGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMGV
RHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA

Ligand information

>8i0p Chain z (length=25) Species: 9606 (Homo sapiens)

AAAAAAAAAAAAAAAAAAAAAAAGA

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i0p Molecular Basis for the activation of Human spliceosome
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R686 M690
• Binding residue (residue number reindexed from 1): R612 M616

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:8i0p, PDBe:8i0p, PDBj:8i0p
• PDBsum: 8i0p
• PubMed: 39068178
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)