Structure of PDB 5wsg Chain A

Receptor sequence

>5wsgA (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: 5wsg Structure of a yeast step II catalytically activated spliceosome
• Chain: A
• Resolution: 4.0 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	peptide	A	N343 N344 A345 P347 P354 E359 R380 K1362 D1411 I1422 T1423 H1424 F1425 R1426 A1427 G1428	N217 N218 A219 P221 P228 E233 R254 K1218 D1267 I1278 T1279 H1280 F1281 R1282 A1283 G1284
BS02	rna	A	E512 V520 R614 Y667 R668 Y671 S1377 K1378 M1379 P1380 Y1620	E368 V376 R470 Y523 R524 Y527 S1233 K1234 M1235 P1236 Y1476
BS03	rna	A	Y128 K190 R284 T296 S297 K333 K334 K340 F352 E353 L355 R358 W402 F484 R488 R495 D498 K503 N532 E533 H535 L538 P539 T540 N541 K549 K670 Y671 K672 H675 R709 N713 R716 G717 P720 L721 H839 R1366	Y2 K64 R158 T170 S171 K207 K208 K214 F226 E227 L229 R232 W276 F340 R344 R351 D354 K359 N388 E389 H391 L394 P395 T396 N397 K405 K526 Y527 K528 H531 R565 N569 R572 G573 P576 L577 H695 R1222
BS04	rna	A	K152 T156 K586 K608 E609 G616 S618 Y725 N728 R732 R737 K743 T744 T746 R749 A752 L756 F1866	K26 T30 K442 K464 E465 G472 S474 Y581 N584 R588 R593 K599 T600 T602 R605 A608 L612 F1712
BS05	rna	A	D755 Q784 S787 R791 K794 K847 R851 R854 N930 A931 R934 K1093 D1094 F1587 K1588	D611 Q640 S643 R647 K650 K703 R707 R710 N786 A787 R790 K949 D950 F1443 K1444
BS06	rna	A	V1860 N1869 V1870 K1903	V1706 N1715 V1716 K1749
BS07	rna	A	G1324 S1325 K1330 T1337 F1525 H1592 A1593 R1595 T1596 Q1647	G1180 S1181 K1186 T1193 F1381 H1448 A1449 R1451 T1452 Q1503

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:5wsg, PDBe:5wsg, PDBj:5wsg
• PDBsum: 5wsg
• PubMed: 27980089
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)