Structure of PDB 9fmd Chain A

Receptor sequence
>9fmdA (length=2250) Species: 9606 (Homo sapiens) [Search protein sequence]
MSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKEDMPPEHVRKIIRDHG
DMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITG
AISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEP
PLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGST
YQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIP
GGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLP
HHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDD
DEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDI
PLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFR
SFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNL
KPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQL
ADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKG
PGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTK
QRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANI
PWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKK
NLGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSP
IPFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNP
HEALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQ
YLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECN
VMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNH
TNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSF
QDIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNEN
IVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSF
VSVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKER
TAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYF
REAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGG
LGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQP
WESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQ
KDRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDM
IQALGGVEGILEHTLFKGTYFPTWEGLFWETNAQRSGLNQIPNRRFTLWW
SPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHES
IVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWN
VSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYT
TDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANP
ALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRV
TIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAK
WKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSE
LQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLIL
ILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLIL
ADYGKKNNVNVASLTQSEIRDIILGMEISAPFSSKTEWRVRAISAANLHL
RTNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPD
NPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWIHTQPNES
PQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAYKLTPSGY
EWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMG
VRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA
3D structure
PDB9fmd Mechanism for the initiation of spliceosome disassembly.
ChainA
Resolution3.3 Å
3D
structure
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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 E678 D682 R686 K702 N704 K705 R707 T708 Q711 S714 W717 K721 K746 W750 T770 K773 K774 R778 R781 N857 Q858 R861 K1020 E654 D658 R662 K678 N680 K681 R683 T684 Q687 S690 W693 K697 K722 W726 T746 K749 K750 R754 R757 N833 Q834 R837 K996
BS02 rna A K50 G52 F53 V54 D55 A56 H97 K101 I132 W134 R217 G222 S223 T224 K267 F279 E280 R409 R417 R419 R420 D423 P425 K428 K452 N457 H461 P464 K465 A466 Q467 K468 K469 R474 K595 Y596 K597 R600 Q601 R635 F639 F640 R642 G643 P646 L647 V767 D768 K1294 I1301 K26 G28 F29 V30 D31 A32 H73 K77 I108 W110 R193 G198 S199 T200 K243 F255 E256 R385 R393 R395 R396 D399 P401 K404 K428 N433 H437 P440 K441 A442 Q443 K444 K445 R450 K571 Y572 K573 R576 Q577 R611 F615 F616 R618 G619 P622 L623 V743 D744 K1270 I1277
BS03 rna A Q39 K48 K480 K511 E534 K536 K537 R539 G541 A543 W651 N654 R658 R663 K666 V668 K670 T671 T673 Q675 R676 S679 L683 T1793 N1797 T1799 K1801 A1828 K1831 Q15 K24 K456 K487 E510 K512 K513 R515 G517 A519 W627 N630 R634 R639 K642 V644 K646 T647 T649 Q651 R652 S655 L659 T1755 N1759 T1761 K1763 A1790 K1793
BS04 rna A P274 K278 R309 V441 R444 V445 Q448 R539 Y592 R593 Y596 R603 S1305 K1306 M1307 P1308 H1352 S1524 Y1548 V1549 G1564 K1565 P250 K254 R285 V417 R420 V421 Q424 R515 Y568 R569 Y572 R579 S1281 K1282 M1283 P1284 H1328 S1486 Y1510 V1511 G1526 K1527
BS05 rna A R82 H83 N512 T532 K533 K536 A1521 Q1522 I1790 L1798 T1800 K1831 R1832 R1865 R58 H59 N488 T508 K509 K512 A1483 Q1484 I1752 L1760 T1762 K1793 R1794 R1827
BS06 IHP A R163 K442 Y580 H584 K609 H610 Y613 Y614 K623 R139 K418 Y556 H560 K585 H586 Y589 Y590 K599
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:9fmd, PDBe:9fmd, PDBj:9fmd
PDBsum9fmd
PubMed38925148
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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