Structure of PDB 8qp9 Chain A

Receptor sequence

>8qp9A (length=1916) Species: 9606 (Homo sapiens)

KEDMPPEHVRKIIRDHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVP
VLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFP
PFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSR
KYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSK
ALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFP
YLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHREPLPD
DDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALD
IPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLF
RSFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFN
LKPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQ
LADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGK
GPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARSHFDLELRAAVMHDI
LDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKVPGLPTPIENMILRYV
KAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLTRLYLKAEQERQHN
YLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLILAL
ERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKE
VGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPA
DTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLESRFEKMYEKIDLTLL
NRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGIIRGLQFASFIVQY
YGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATEAAHPIRLFCRYID
RIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARMRLM
KHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFE
CRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNR
VRQILMASGSTTFTKIVNKWNTALIGLMTYFREAVVNTQELLDLLVKCEN
KIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSMGHVLIPQSDLRWS
KQTDVGITHFRSQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEAIAQN
RRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQ
NPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEG
LFWEKASGFEESMKWKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVG
FQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQE
LDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSKD
VMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPTG
VLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRKG
LQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTT
KPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIR
SLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVE
KFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRA
KVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILADYGKKNNVNVA
SLTQSEIRDIILGMEI

3D structure

• PDB: 8qp9 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	peptide	A	T1613 I1614	T1513 I1514
BS02	rna	A	G222 S223 T224 F279 E280 R409 D423 P425 N457 P463 P464 K465 A466 Y596 M599 F639 G643 P646	G155 S156 T157 F212 E213 R336 D350 P352 N384 P390 P391 K392 A393 Y523 M526 F566 G570 P573

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:8qp9, PDBe:8qp9, PDBj:8qp9
• PDBsum: 8qp9
• PubMed: 38778104
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)