Structure of PDB 8qpe Chain A

Receptor sequence

>8qpeA (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: 8qpe Structural insights into the cross-exon to cross-intron spliceosome switch
• Chain: A
• Resolution: 3.1 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	Q858 Q888	Q788 Q818
BS02	rna	A	Q57 H97 K101 I132 W134 R217 G222 S223 T224 K267 F279 E280 V283 R409 R417 R419 R420 D423 P425 K428 K452 N457 K460 H461 P464 K465 A466 Q467 K468 K469 R470 R474 N542 Y594 K595 Y596 K597 R600 Q601 M604 R635 F639 F640 R642 G643 P646 T766 K1294 T1297 M1307	Q2 H42 K46 I77 W79 R162 G167 S168 T169 K212 F224 E225 V228 R354 R362 R364 R365 D368 P370 K373 K397 N402 K405 H406 P409 K410 A411 Q412 K413 K414 R415 R419 N487 Y539 K540 Y541 K542 R545 Q546 M549 R580 F584 F585 R587 G588 P591 T696 K1224 T1227 M1237
BS03	rna	A	E534 F1509 M1513 Q1522 I1529 R1532 D1556 L1557 K1570 I1571 I1574 Q1575 R1578 A1579 H1580 Q2032 Q2038 N2048 K2049 H2050 T2056 S2057 T2058 T2059 S2060	E479 F1439 M1443 Q1452 I1459 R1462 D1486 L1487 K1500 I1501 I1504 Q1505 R1508 A1509 H1510 Q1962 Q1968 N1978 K1979 H1980 T1986 S1987 T1988 T1989 S1990
BS04	rna	A	T532 K533 K536 R539 R593 S1305 K1306 F1551 H1563 G1564 K1565	T477 K478 K481 R484 R538 S1235 K1236 F1481 H1493 G1494 K1495
BS05	IHP	A	K442 H584 K609 H610 Y613 Y614 K623 G624	K387 H529 K554 H555 Y558 Y559 K568 G569

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