Structure of PDB 7abf Chain A

Receptor sequence

>7abfA (length=1656) Species: 9606 (Homo sapiens)

PEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQ
IRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFK
RMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQP
LRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKA
FFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEY
KIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHR
HSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFN
LRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHR
PPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKN
LNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHV
QYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLI
YYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQFEG
RVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIP
WKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKN
LGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPI
PFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPH
EALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQY
LWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNV
MLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHT
NSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQ
DIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENI
VGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFV
SVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERT
AQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFR
EAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGL
GMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPW
ESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQK
DRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMI
QALGGVEGILEHTLFKGTYFPTWEGLFWQIPNRRFTLWWSPTINRANVYV
GFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQ
ELDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSK
DVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPT
GVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRK
GLQLYS

3D structure

• PDB: 7abf Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
• Chain: A
• Resolution: 3.9 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	W134 F279 E280 R419 N457 H461 R462 P463 P464 Y471 R474 Y594 K595 Y596 K597 R635 F639 R642 G643 L647 M1307	W72 F217 E218 R357 N395 H399 R400 P401 P402 Y409 R412 Y532 K533 Y534 K535 R573 F577 R580 G581 L585 M1232
BS02	rna	A	K533 R539 F540 N542 A543 W651 R658 R663 L1557 I1571 H1580 R1617	K471 R477 F478 N480 A481 W589 R596 R601 L1458 I1472 H1481 R1518
BS03	rna	A	R82 H509 N512 T531 T532 Q587 Y592 R593 Y596 M599 S1305 F1551 H1563 G1564	R20 H447 N450 T469 T470 Q525 Y530 R531 Y534 M537 S1230 F1452 H1464 G1465
BS04	IHP	A	Y580 H610 Y613	Y518 H548 Y551

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