Structure of PDB 5y88 Chain A

Receptor sequence

>5y88A (length=1903) Species: 559292 (Saccharomyces cerevisiae S288C)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMV
RAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNK
TKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLD
YNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNV
DAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKN
LGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKT
TTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWK
ANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTM
VKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRS
FSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAY
DNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAY
LDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRG
QSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKD
MSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEF
MQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPN
FENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWE
NAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTK
QRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFT
YFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKEL
GGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYI
TTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTL
FQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRT
DVIQALGGIETILEHTLFKGTGFNSWEGLFWENRRFTLWWSPTINRANVY
VGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDICQILD
GELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPSLLHET
NDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSP
TGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVLRERIR
KGLQIYQYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTL
NPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQ
IIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKAT
EPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTI
TIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDI
ILG

3D structure

• PDB: 5y88 Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae
• Chain: A
• Resolution: 3.46 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	Y128 K190 T205 R207 R284 T296 S297 K333 K334 K340 F352 E353 L355 W402 F484 R488 R495 D498 K503 K527 N532 H535 L538 P539 N541 K549 K552 K670 Y671 K672 H675 R709 N713 R716 G717 H839 K842 M1321 R1366	Y2 K64 T79 R81 R158 T170 S171 K207 K208 K214 F226 E227 L229 W276 F340 R344 R351 D354 K359 K383 N388 H391 L394 P395 N397 K405 K408 K526 Y527 K528 H531 R565 N569 R572 G573 H695 K698 M1177 R1222
BS02	rna	A	K152 K555 K586 E609 K611 R614 G616 S618 Y725 N728 R732 R737 K743 T744 Q748 R749	K26 K411 K442 E465 K467 R470 G472 S474 Y581 N584 R588 R593 K599 T600 Q604 R605
BS03	rna	A	D755 K777 R780 S787 K846 K847 R851 R854 R934 K1093 D1094	D611 K633 R636 S643 K702 K703 R707 R710 R790 K949 D950
BS04	IHP	A	R236 K517 H659 K684 Y688 K697 Y1620	R110 K373 H515 K540 Y544 K553 Y1450

Gene Ontology

Molecular Function

• GO:0000386 second spliceosomal transesterification activity
• GO:0003723 RNA binding
• GO:0003729 mRNA 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:0097157 pre-mRNA intronic binding

Biological Process

• GO:0000244 spliceosomal tri-snRNP complex assembly
• GO:0000350 generation of catalytic spliceosome for second transesterification step
• GO:0000387 spliceosomal snRNP assembly
• GO:0000389 mRNA 3'-splice site recognition
• GO:0000395 mRNA 5'-splice site recognition
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing

Cellular Component

• GO:0005634 nucleus
• GO:0005681 spliceosomal complex
• GO:0005682 U5 snRNP
• GO:0005737 cytoplasm
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071013 catalytic step 2 spliceosome

External links

• PDB: RCSB:5y88, PDBe:5y88, PDBj:5y88
• PDBsum: 5y88
• PubMed: 28919079
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)