Structure of PDB 7abg Chain A

Receptor sequence

>7abgA (length=2174) Species: 9606 (Homo sapiens)

PEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQ
IRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFK
RMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQP
LRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKA
FFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEY
KIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHR
HSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFN
LRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHR
PPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKN
LNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHV
QYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLI
YYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARVESH
FDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKVPG
LPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLT
RLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPL
SYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSR
IKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEA
DKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLESR
FEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGI
IRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATE
AAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNN
KKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSK
DNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFL
RVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAVVN
TQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSM
GHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFI
DSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTL
AYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGG
VEGILEHTLFKGTYFPTWEGLFWQIPNRRFTLWWSPTINRANVYVGFQVQ
LDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDAL
EIETVQKETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSKDVMDS
TTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIA
IDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRKGLQLY
SELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLF
LKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGM
LDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFN
LYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIW
PTLTDEEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIIITSTTSN
YETQTFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKETGYTYILPKNVL
KKFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPG
QLPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKT
IIITCSFTPGSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQM
LLSDRFLGFFMVPAQSSWNYNFMGVRHDPNMKYELQLANPKEFYHEVHRP
SHFLNFALLQEGEVYSADREDLYA

3D structure

• PDB: 7abg Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
• Chain: A
• Resolution: 7.8 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	N221 G222 S223 T224 F279 N457 P464 K465 Y594 K595 K597 R642 G643	N159 G160 S161 T162 F217 N395 P402 K403 Y532 K533 K535 R580 G581
BS02	rna	A	T531 T532 Y596 S1305 F1551 G1564	T469 T470 Y534 S1225 F1447 G1460
BS03	rna	A	T532 K533 R539 N542 A543 D1556 I2055	T470 K471 R477 N480 A481 D1452 I1894

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:7abg, PDBe:7abg, PDBj:7abg
• PDBsum: 7abg
• PubMed: 33243851
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)