Structure of PDB 8i0u Chain A

Receptor sequence

>8i0uA (length=1969) 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
EGILEHTLFKGTYFPTWEGLFWEKWKKLTNAQRSGLNQIPNRRFTLWWSP
TINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHESIV
MDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWNVS
RPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYTTD
NMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPAL
YVLRERIRKGLQLYSSEPTQNYGELFSNQIIWFVDDTNVYRVTIHKTFEG
NLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVA
ALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQAC
LKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVN
NDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILADYGKKNN
VNVASLTQSEIRDIILGME

3D structure

• PDB: 8i0u Molecular basis for the activation of human spliceosome
• Chain: A
• Resolution: 3.3 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	I132 W134 N221 T224 K267 E280 R417 R419 R420 P425 K428 N457 H461 P464 Q467 K469 R474 K595 Y596 K597 R635 F639 R642 G643 V767 R1298	I108 W110 N197 T200 K243 E256 R386 R388 R389 P394 K397 N426 H430 P433 Q436 K438 R443 K564 Y565 K566 R604 F608 R611 G612 V736 R1267
BS02	rna	A	K48 E534 K536 R539 G541 A543 W651 N654 R658 R663 T671 Q675 R676 S679	K24 E503 K505 R508 G510 A512 W620 N623 R627 R632 T640 Q644 R645 S648
BS03	rna	A	R82 H83 P274 K278 C435 V441 Q448 T532 K533 R535 R539 Y592 R593 Y596 S1305 K1306 M1307 P1308	R58 H59 P250 K254 C404 V410 Q417 T501 K502 R504 R508 Y561 R562 Y565 S1274 K1275 M1276 P1277
BS04	rna	A	D682 Q703 K705 R707 Q711 S714 K774 R778 R781 Q858 R861 K1020 D1021	D651 Q672 K674 R676 Q680 S683 K743 R747 R750 Q827 R830 K989 D990
BS05	peptide	A	S1524 I1571 R1578	S1484 I1531 R1538
BS06	IHP	A	K442 H584 K609 H610 Y613 Y614 K623	K411 H553 K578 H579 Y582 Y583 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:8i0u, PDBe:8i0u, PDBj:8i0u
• PDBsum: 8i0u
• PubMed: 39068178
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)