Structure of PDB 8r08 Chain A

Receptor sequence
>8r08A (length=2178) Species: 9606 (Homo sapiens) [Search protein sequence]
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
SLTQSEIRDIILGMEISSKTEWRVRAISAANLHLRTNHIYVSSDDIKETY
TYILPKNVLKKFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWG
THQTVHLPGQLPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMAD
NPSWDGEKTIIITCSFTPGSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYL
PSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMGVRHDPNMKYELQLANPK
EFYHEVHRPSHFLNFALVYSADREDLYA
3D structure
PDB8r08 Structural insights into the cross-exon to cross-intron spliceosome switch
ChainA
Resolution6.1 Å
3D
structure
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Enzymatic activity
Enzyme Commision number ?
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 D423 P425 N457 P463 P464 K465 A466 Y596 M599 F639 G643 P646 G155 S156 T157 F212 E213 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8r08, PDBe:8r08, PDBj:8r08
PDBsum8r08
PubMed38778104
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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