Structure of PDB 8h6l Chain 5B

Receptor sequence

>8h6l5B (length=2253) Species: 9606 (Homo sapiens)

AQKEDMPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLEN
MPMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREK
RDRRHFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLD
WFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYF
YLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIR
QPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPL
INPISHRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALL
WAPRPFNLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYV
LNALKHRPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLN
LLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTK
LVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMC
KDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNL
LARQFEGQRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAW
RCWKANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATV
DKTVCKKNLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWL
ESRRFSPIPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLI
EQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKI
TDAYLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWE
TSEGECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVI
NYKDMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQM
PNDFLSFQDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEH
PDPNNENIVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTT
VQWENSFVSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQ
NEVTKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTAL
IGLMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFY
TPKELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPN
LYRYIQPWESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIP
RINTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNL
NNYRTDMIQALGGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKK
LTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIP
TLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPR
KSYKMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLR
WGDYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGN
WFPGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQN
YGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQL
FLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKG
MLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLF
NLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHI
WPTLTDEEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEIS
APSQQRQQIAEIEKQTKEQSQLTATQTRTVNKHGDEIITSTTSNYETQTF
SSKTEWRVRAISAANLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICI
SDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHE
YLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCS
FTPGSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRF
LGFFMVPAQSSWNYNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNF
ALL

3D structure

• PDB: 8h6l Structural Insights into Human Exon-defined Spliceosome Prior to Activation
• Chain: 5B
• Resolution: 2.6 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	5B	T532 K533 R535 K536 R539 Y596 S1305 K1306 F1551 H1563 K1565	T477 K478 R480 K481 R484 Y541 S1238 K1239 F1484 H1496 K1498
BS02	rna	5B	H97 W134 R217 G222 S223 T224 K267 E280 L282 R409 R417 R419 R420 D423 P425 K452 N457 K460 H461 P464 K465 A466 Q467 K468 K469 R470 R474 K595 Y596 K597 R600 R635 F639 R642 G643 P646 I1301 M1307	H42 W79 R162 G167 S168 T169 K212 E225 L227 R354 R362 R364 R365 D368 P370 K397 N402 K405 H406 P409 K410 A411 Q412 K413 K414 R415 R419 K540 Y541 K542 R545 R580 F584 R587 G588 P591 I1234 M1240
BS03	rna	5B	K537 F1509 Q1522 D1556 L1557 K1570 I1574 Q1575 R1578 A1579 R1617 Q2032 T2059 S2060	K482 F1442 Q1455 D1489 L1490 K1503 I1507 Q1508 R1511 A1512 R1550 Q1965 T1992 S1993
BS04	rna	5B	Q858 R861 T887 A890 F891	Q791 R794 T820 A823 F824
BS05	IHP	5B	K442 H584 K606 K609 Y613	K387 H529 K551 K554 Y558

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0008233 peptidase activity
• GO:0008237 metallopeptidase 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:8h6l, PDBe:8h6l, PDBj:8h6l
• PDBsum: 8h6l
• PubMed: 38658629
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)