Structure of PDB 8rc0 Chain A

Receptor sequence

>8rc0A (length=2153) 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
QAMAKIMKANPALYVLRERIRKGLQLYEPYLSSQNYGELFSNQIIWFVDD
TNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKR
LGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNI
VIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTA
FSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQ
LKDLILADYGKKNNVNVASLTQSEIRDIILGMEIFSSKTEWRVRAISAAN
LHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYLYGVS
PPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWIHTQP
NESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAYKLTP
SGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYN
FMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADRED
LYA

3D structure

• PDB: 8rc0 Structure of the human 20S U5 snRNP.
• Chain: A
• Resolution: 3.2 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 I132 W134 R217 N221 G222 T224 F279 E280 R417 R419 R420 D423 K428 K452 N457 H461 P463 P464 K465 A466 Q467 K468 K469 R470 R474 K595 Y596 K597 M599 Q601 R603 R635 F639 F640 R642 G643 P646	H29 I64 W66 R149 N153 G154 T156 F211 E212 R343 R345 R346 D349 K354 K378 N383 H387 P389 P390 K391 A392 Q393 K394 K395 R396 R400 K521 Y522 K523 M525 Q527 R529 R561 F565 F566 R568 G569 P572

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:8rc0, PDBe:8rc0, PDBj:8rc0
• PDBsum: 8rc0
• PubMed: 38467877
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)