Structure of PDB 8q91 Chain A

Receptor sequence

>8q91A (length=1627) Species: 9606 (Homo sapiens)

KEDMPPEHVRKIIRDHKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPV
LYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPP
FDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRK
YVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKA
LNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPY
LYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHREPLPDD
DEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDI
PLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFR
SFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNL
KPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQL
ADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKG
PGCGFWAAGWRVWLFFMRGITPLLERWLGNLLAHFDLELRAAVMHDILDM
MPEGIKQNKARTILQHLSEAWRCWKANIPWKVPGLPTPIENMILRYVKAK
ADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLTRLYLKAEQERQHNYLK
DGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLILALERL
KEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKEVGI
EFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPADTE
PPPLLVYKWCQGINNLQDVWETSEGECNVMLESRFEKMYEKIDLTLLNRL
LRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGIIRGLQFASFIVQYYGL
VMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATEAAHPIRLFCRYIDRIH
IFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARMRLMKHD
VNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFECRI
LPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNRVRQ
ILMASGSTTFTKIVNKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQ
TRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSMGHVLIPQSDLRWSKQT
DVGITHFRSQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEAIAQNRRL
TLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQNPF
WWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEGLFW
EKPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIF
RAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCA
DILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIE
RYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQ
QAMAKIMKANPALYVLRERIRKGLQLY

3D structure

• PDB: 8q91 Structure of the human 20S U5 snRNP.
• Chain: A
• Resolution: 3.1 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	K101 W134 R217 N221 G222 S223 T224 K267 E280 R409 R419 R420 D423 P425 K428 N457 H461 R462 P463 P464 K465 A466 Q467 K468 K469 R470 R474 K595 Y596 K597 M599 Q601 R603 R635 F639 F640 R642 G643 P646	K33 W66 R149 N153 G154 S155 T156 K199 E212 R335 R345 R346 D349 P351 K354 N383 H387 R388 P389 P390 K391 A392 Q393 K394 K395 R396 R400 K521 Y522 K523 M525 Q527 R529 R561 F565 F566 R568 G569 P572
BS02	peptide	A	H1209 K1210 D1211 R1275 V1279 V1289 E1292 N1293 G1331 H1332 V1333 Y1369 R1370 Y1371 I1372 P1374 E1409 W1412 D1413 R1414 N1469	H1113 K1114 D1115 R1179 V1183 V1193 E1196 N1197 G1235 H1236 V1237 Y1266 R1267 Y1268 I1269 P1271 E1306 W1309 D1310 R1311 N1366

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:8q91, PDBe:8q91, PDBj:8q91
• PDBsum: 8q91
• PubMed: 38467877
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)