Structure of PDB 5ylz Chain A

Receptor sequence

>5ylzA (length=1931) 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
DVIQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQ
RTGLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKIS
LIQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKM
NSSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYD
SHDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGL
KPLIQNSMRTIMKANPALYVLRERIRKGLQIYQSSYAELFNNDIKLFVDD
TNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVWAGQKR
LSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNI
AIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRISSYTA
FSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWITIESQ
MRDLILTEYGRKYNVNISALTQTEIKDIILG

3D structure

• PDB: 5ylz Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae
• Chain: A
• Resolution: 3.6 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 R284 T296 S297 K333 K334 K340 F352 E353 L355 F484 R488 R495 D498 K503 K527 N532 H535 P539 N541 K549 K670 Y671 K672 R709 N713 R716 G717 H839	Y2 K64 T79 R158 T170 S171 K207 K208 K214 F226 E227 L229 F340 R344 R351 D354 K359 K383 N388 H391 P395 N397 K405 K526 Y527 K528 R565 N569 R572 G573 H695
BS02	rna	A	K152 T156 K586 E609 K611 G616 S618 Y725 N728 R732 R737 T744 Q748 R749 Y753 L756	K26 T30 K442 E465 K467 G472 S474 Y581 N584 R588 R593 T600 Q604 R605 Y609 L612
BS03	rna	A	K351 E512 K519 Q523 K608 K611 R614 Y667 R668 Y671 G1324 S1377 M1379 P1380 K1588 T1591 H1592 Q1594 R1595 G1597 Y1620 K1637 N1869 V1870 T1872 R1904	K225 E368 K375 Q379 K464 K467 R470 Y523 R524 Y527 G1180 S1233 M1235 P1236 K1444 T1447 H1448 Q1450 R1451 G1453 Y1476 K1493 N1715 V1716 T1718 R1750
BS04	rna	A	D751 D755 R780 Q784 S787 K846 K847 R851 R854 N930 R934 K1093 D1094 K1588	D607 D611 R636 Q640 S643 K702 K703 R707 R710 N786 R790 K949 D950 K1444
BS05	peptide	A	N343 P347 E353 P357 E359 R380 K1362 T1365 I1422 T1423 H1424 F1425 R1426 A1427 G1428	N217 P221 E227 P231 E233 R254 K1218 T1221 I1278 T1279 H1280 F1281 R1282 A1283 G1284
BS06	IHP	A	R236 K517 H659 K684 K697 G698	R110 K373 H515 K540 K553 G554

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:5ylz, PDBe:5ylz, PDBj:5ylz
• PDBsum: 5ylz
• PubMed: 29153833
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)