Structure of PDB 8q7v Chain A

Receptor sequence

>8q7vA (length=1645) Species: 9606 (Homo sapiens)

MSEEKLQEKARKWQQLQAKRYAEEDMPPEHVRKIIRDHKRVYLGALKYMP
HAVLKLLENMPMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGS
MWIMMRREKRDRFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPE
EDAPVLDWFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTD
LVDDNYFYLFDLKAFFTSKALNMAIPGGPKFEPLDEDWNEFNDINKIIIR
QPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPL
INPISHREPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPF
NLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKH
RPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRK
NLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSH
VQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHL
IYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLASHFD
LELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKVPGLP
TPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLTRL
YLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSY
KHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIK
RHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEADK
RRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLESRFE
KMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGIIR
GLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATEAA
HPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKK
CWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDN
PNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFLRV
DDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAVVNTQ
ELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSMGH
VLIPQSDLRWSKQTDVGITHFRSQLIPNLYRYIQPWESEFIDSQRVWAEY
ALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVR
TDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTL
FKGTYFPTWEGLFWEKNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGI
FMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQ
KETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKY
WIDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYN
LHSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLYS

3D structure

• PDB: 8q7v Structural basis of human U5 snRNP late biogenesis and recycling.
• Chain: A
• Resolution: 3.8 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	H97 R217 G222 T224 E280 R409 R417 R419 P425 K428 N457 H461 R462 P464 K465 A466 Q467 K469 R470 R474 K477 Y596 K597 M599 R635 F639 R642 G643 L647	H51 R169 G174 T176 E232 R348 R356 R358 P364 K367 N396 H400 R401 P403 K404 A405 Q406 K408 R409 R413 K416 Y535 K536 M538 R574 F578 R581 G582 L586
BS02	peptide	A	H1209 R1275 D1286 V1289 N1293 R1310 G1331 H1332 V1333 Y1369 R1370 Y1371 I1372 P1374 W1412 D1413 R1414 N1466 N1469	H1127 R1193 D1204 V1207 N1211 R1228 G1249 H1250 V1251 Y1280 R1281 Y1282 I1283 P1285 W1323 D1324 R1325 N1377 N1380
BS03	peptide	A	G798 P799 A803 D989 T991 A1011 N1014	G716 P717 A721 D907 T909 A929 N932

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:8q7v, PDBe:8q7v, PDBj:8q7v
• PDBsum: 8q7v
• PubMed: 38467876
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)