Structure of PDB 6j6n Chain A

Receptor sequence

>6j6nA (length=1913) Species: 559292 (Saccharomyces cerevisiae S288C)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIPHFGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKG
KMVRAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTN
HNKTKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYL
HLDYNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRL
GNVDAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKF
NKNLGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEI
VKTTTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWR
CWKANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVE
KTMVKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLE
SRSFSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIE
EAYDNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKIT
DAYLDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDV
SRGQSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVIN
FKDMSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNP
NEFMQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENP
DPNFENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSI
KWENAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDE
RTKQRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLIS
LFTYFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTP
KELGGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIF
RYITTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRI
STLFQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNA
YRTDVIQALGGIETILEHTLFKGTGFNSWEGLFWEKSQIPNRRFTLWWSP
TINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIV
FDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVS
KPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTD
NVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPAL
YVLRERIRKGLQIYQSSYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVAT
KAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVR
SLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSID
KLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESA
KMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNIS
ALTQTEIKDIILG

3D structure

• PDB: 6j6n Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
• Chain: A
• Resolution: 3.86 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 F352 E353 P354 R380 S381 K1362 T1365 D1411 T1423 H1424 F1425 R1426 A1427 G1428	N217 N218 A219 F226 E227 P228 R254 S255 K1221 T1224 D1270 T1282 H1283 F1284 R1285 A1286 G1287
BS02	rna	A	V516 Q523 T607 R610 R614 Y667 R668 Y671 R678 S925 K926 V927 K1330 S1377 K1378 M1379 P1380 K1535 S1599 Q1600 Y1620 G1636 K1637	V375 Q382 T466 R469 R473 Y526 R527 Y530 R537 S784 K785 V786 K1189 S1236 K1237 M1238 P1239 K1394 S1437 Q1438 Y1458 G1474 K1475
BS03	rna	A	Y128 L173 T205 R207 R284 G295 T296 S297 K299 K325 K340 F352 E353 L355 R358 W402 F484 R488 R495 D498 K503 E533 H535 T537 P539 N541 K544 K546 K549 K552 K670 Y671 K672 H675 R709 N713 R716 G717 P720 H839 L1373	Y2 L47 T79 R81 R158 G169 T170 S171 K173 K199 K214 F226 E227 L229 R232 W276 F343 R347 R354 D357 K362 E392 H394 T396 P398 N400 K403 K405 K408 K411 K529 Y530 K531 H534 R568 N572 R575 G576 P579 H698 L1232
BS04	rna	A	S151 K152 M153 K586 E609 K611 R614 G616 S618 Y725 N728 R732 R737 I741 K743 T744 T746 Q748 R749 L756	S25 K26 M27 K445 E468 K470 R473 G475 S477 Y584 N587 R591 R596 I600 K602 T603 T605 Q607 R608 L615
BS05	rna	A	D755 R759 R780 Q784 S787 W790 K794 K847 R851 R854 R928 L929 N930 A931 R934 K1093 D1094	D614 R618 R639 Q643 S646 W649 K653 K706 R710 R713 R787 L788 N789 A790 R793 K952 D953
BS06	IHP	A	R236 K517 K684 K697	R110 K376 K543 K556

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:6j6n, PDBe:6j6n, PDBj:6j6n
• PDBsum: 6j6n
• PubMed: 30879786
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)