Structure of PDB 8qzs Chain A

Receptor sequence

>8qzsA (length=2247) Species: 9606 (Homo sapiens)

AQKEDMPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLEN
MPMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREK
RDRRHFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLD
WFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYF
YLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIR
QPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPL
INPISHRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALL
WAPRPFNLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYV
LNALKHRPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLN
LLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTK
LVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMC
KDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNL
LARQFRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCW
KANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKT
VCKKNLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESR
RFSPIPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQA
YDNPHEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDA
YLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSE
GECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYK
DMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPND
FLSFQDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDP
NNENIVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQW
ENSFVSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEV
TKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGL
MTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPK
ELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYR
YIQPWESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRIN
TLFQKDRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNY
RTDMIQALGGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLTN
AQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLK
ISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSY
KMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGD
YDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFP
GSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYGE
LFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLK
IIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLD
PLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLY
DDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPT
LTDEEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEISAPS
QQRQQIAEIEKQTKEQSQLTATQTRTVNKHGDEIITSTTSNYETQTFSSK
TEWRVRAISAANLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICISDL
RAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLK
EMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTP
GSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGF
FMVPAQSSWNYNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNF

3D structure

• PDB: 8qzs Structural insights into the cross-exon to cross-intron spliceosome switch
• Chain: A
• Resolution: 4.1 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	G222 T224 F279 D423 P425 N457 P464 K465 A466 Q467 K469 Y594 K595 Y596 K597 F639 F640 R642 G643 P646	G167 T169 F224 D368 P370 N402 P409 K410 A411 Q412 K414 Y539 K540 Y541 K542 F584 F585 R587 G588 P591
BS02	rna	A	D1556 R1578 A1579 N2048 S2057 T2058 S2060	D1486 R1508 A1509 N1978 S1987 T1988 S1990
BS03	rna	A	S1305 K1306 F1551 H1563 G1564 K1565	S1235 K1236 F1481 H1493 G1494 K1495

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