Structure of PDB 7dvq Chain A

Receptor sequence

>7dvqA (length=2223) Species: 9606 (Homo sapiens)

EEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKEDMPPEHVRKIIRDHGDM
TNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITGAI
SFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPPL
DYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTYQ
RWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGG
PKFEPLVRDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLPHHVHLTWYH
TPNVVFIKTEDPDLPAFYFDPLINPISFELPEFVEPFLKDTPLYTDNTAN
GIALLWAPRPFNLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKL
LKYYVLNALKHRPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQG
YNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREV
LRLTKLVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMR
QIRMCKDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLER
WLGNLLARQFEGRHSKGVAKTVTKQRVESHFDLELRAAVMHDILDMMPEG
IKQNKARTILQHLSEAWRCWKANIPWKVPGLPTPIENMILRYVKAKADWW
TNTAHYNRERIRRGATVDKTVCKKNLGRLTRLYLKAEQERQHNYLKDGPY
ITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLILALERLKEAY
SVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMD
LYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPADTEPPPL
LVYKWCQGINNLQDVWETSEGECNVMLESRFEKMYEKIDLTLLNRLLRLI
VDHNIADYMTAKNNVVINYKDMNHTNSYGIIRGLQFASFIVQYYGLVMDL
LVLGLHRASEMAGPPQMPNDFLSFQDIATEAAHPIRLFCRYIDRIHIFFR
FTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARMRLMKHDVNLG
RAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFECRILPKC
RTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNRVRQILMA
SGSTTFTKIVNKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQTRIK
IGLNSKMPSRFPPVVFYTPKELGGLGMLSMGHVLIPQSDLRWSKQTDVGI
THFRSGMSHEEDQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEAIAQN
RRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQ
NPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEG
LFWEKASGFEQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIF
MHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQK
ETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYW
IDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNL
HSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYSSEPTEP
YLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFN
PRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQI
IVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATE
PQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTI
TEPHHIWPTLTDEEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDII
LGMEFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKETGYTYILPKNVLK
KFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQ
LPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTI
IITCSFTPGSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQML
LSDRFLGFFMVPAQSSWNYNFMGVRHDPNMKYELQLANPKEFYHEVHRPS
HFLNFALLQEGEVYSADREDLYA

3D structure

• PDB: 7dvq Structure of the activated human minor spliceosome.
• Chain: A
• Resolution: 2.89 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	Q57 H97 I132 W134 G222 T224 K267 E280 R284 R409 R417 R419 R420 D423 K428 K452 N457 K460 H461 P464 A466 K468 K469 R470 R474 K595 Y596 K597 R600 R635 F639 R642 G643 P646 V767 D768 R1298	Q31 H71 I106 W108 G196 T198 K241 E254 R258 R359 R367 R369 R370 D373 K378 K402 N407 K410 H411 P414 A416 K418 K419 R420 R424 K545 Y546 K547 R550 R585 F589 R592 G593 P596 V717 D718 R1248
BS02	rna	A	T531 K533 E534 K536 R539 G541 A543 W651 N654 R658 A669 K670 T671 T673 Q675 R676 S679 L683 R707	T481 K483 E484 K486 R489 G491 A493 W601 N604 R608 A619 K620 T621 T623 Q625 R626 S629 L633 R657
BS03	rna	A	K278 H509 R510 N512 T532 K533 Y592 R593 Y596 K1306 M1307 H1352 S1358 Y1548	K252 H459 R460 N462 T482 K483 Y542 R543 Y546 K1256 M1257 H1302 S1308 Y1487
BS04	rna	A	D682 R686 S714 K721 K773 K774 R778 R781 Q858 K1020	D632 R636 S664 K671 K723 K724 R728 R731 Q808 K970
BS05	peptide	A	N270 R309 T310 D1339 L1340 T1351 H1352 F1353 R1354 S1355 G1356	N244 R276 T277 D1289 L1290 T1301 H1302 F1303 R1304 S1305 G1306
BS06	IHP	A	K442 H584 K609 Y613 Y614 K623	K392 H534 K559 Y563 Y564 K573

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:7dvq, PDBe:7dvq, PDBj:7dvq
• PDBsum: 7dvq
• PubMed: 33509932
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)