Structure of PDB 8i0w Chain A

Receptor sequence

>8i0wA (length=2253) Species: 9606 (Homo sapiens)

MSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKEDMPPEHVRKIIRDHG
DMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITG
AISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEP
PLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGST
YQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIP
GGPKFEPLVRDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLPHHVHLTW
YHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDDDEEFELP
EFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDIPLVKNWY
REHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKATKF
FQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLT
TKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGLQYI
FAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKGPGCGFWA
AGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTKQRVESHF
DLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKVPGL
PTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLTR
LYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLS
YKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRI
KRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEAD
KRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLESRF
EKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGII
RGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATEA
AHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNK
KCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKD
NPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFLR
VDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAVVNT
QELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSMG
HVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFID
SQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLA
YDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGV
EGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLTNAQRSGLNQIPN
RRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHL
WQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILL
FASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYAR
AKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMA
KIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVD
DTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQK
RLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPN
IVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYT
AFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEV
QLKDLILADYGKKNNVNVASLTQSEIRDIILGMEFSSKTEWRVRAISAAN
LHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYLYGVS
PPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWIHTQP
NESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAYKLTP
SGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYN
FMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADRED
LYA

3D structure

• PDB: 8i0w Molecular basis for the activation of human spliceosome
• Chain: A
• Resolution: 3.4 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 K267 E280 R409 R417 R419 R420 P425 K452 N457 K460 H461 P464 Q467 K469 R474 K595 Y596 K597 R635 F639 R642 G643 P646 V767 D768 K1306	G198 T200 K243 E256 R378 R386 R388 R389 P394 K421 N426 K429 H430 P433 Q436 K438 R443 K564 Y565 K566 R604 F608 R611 G612 P615 V736 D737 K1275
BS02	rna	A	K48 K80 K511 E534 K537 R539 G541 A543 W651 N654 R658 R663 T671 T673 Q675 R676 S679 R707	K24 K56 K480 E503 K506 R508 G510 A512 W620 N623 R627 R632 T640 T642 Q644 R645 S648 R676
BS03	rna	A	K278 C435 V441 Y592 R593 Y596 S1305 K1306 M1307 P1308 Y1548	K254 C404 V410 Y561 R562 Y565 S1274 K1275 M1276 P1277 Y1517
BS04	rna	A	R82 T532 K533 V852 K853 K1258 K1262 K1425 K1449 K1463 R1523 L1526 N1527 R1578 K1749 R1832 Q1835	R58 T501 K502 V821 K822 K1227 K1231 K1394 K1418 K1432 R1492 L1495 N1496 R1547 K1718 R1801 Q1804
BS05	rna	A	T529 D682 N704 K705 Q711 S714 W717 K774 R778 R781 R855 R861 K1020 D1021 S1253 T1255 K1516 K1517 P1530 N1531 P1567 I1571 N1797 L1798	T498 D651 N673 K674 Q680 S683 W686 K743 R747 R750 R824 R830 K989 D990 S1222 T1224 K1485 K1486 P1499 N1500 P1536 I1540 N1766 L1767
BS06	peptide	A	T1783 R1787 V1788 T1789 I1790 Q1890 L1891 P1892 Q1894 A1895 R1941 H1944	T1752 R1756 V1757 T1758 I1759 Q1859 L1860 P1861 Q1863 A1864 R1910 H1913
BS07	IHP	A	K442 H584 K609 Y613 K623	K411 H553 K578 Y582 K592

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:8i0w, PDBe:8i0w, PDBj:8i0w
• PDBsum: 8i0w
• PubMed: 39068178
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)