Structure of PDB 5lj3 Chain A

Receptor sequence

>5lj3A (length=1922) Species: 4932 (Saccharomyces cerevisiae)

YTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLLE
NMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRRE
KRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVK
DWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNY
YYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRV
PIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPS
LEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKK
WFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNT
KYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKT
LTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIH
YILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFW
QPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKTTTKQRLDAYY
DLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGM
PAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTR
LWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLT
YKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRI
KKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEAD
QRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTL
GEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLI
RGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEK
AHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNR
KCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKN
NPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKV
SEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATE
PLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASH
ILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITTWENEFLDS
QRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAY
DRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIE
TILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQRTGLSQIPNR
RFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLW
QKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITME
SVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRA
KFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRT
IMKANPALYVLRERIRKGLQIYQSSNYAELFNNDIKLFVDDTNVYRVTVH
KTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKT
AEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRL
PFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLR
ALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEY
GRKYNVNISALTQTEIKDIILG

3D structure

• PDB: 5lj3 Cryo-EM structure of the spliceosome immediately after branching.
• Chain: A
• Resolution: 3.8 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 T129 P130 H170 E204 T205 R207 R284 G295 T296 S297 K300 K325 K334 K340 F352 E353 W402 F484 R488 K492 R495 D498 K503 K527 N532 H535 T537 L538 P539 N541 K544 K549 K670 Y671 K672 H675 Q676 R709 N713 F714 R716 G717 P720 H839 V840 E841 K842 N1369 R1370	Y1 T2 P3 H43 E77 T78 R80 R157 G168 T169 S170 K173 K198 K207 K213 F225 E226 W275 F330 R334 K338 R341 D344 K349 K373 N378 H381 T383 L384 P385 N387 K390 K395 K516 Y517 K518 H521 Q522 R555 N559 F560 R562 G563 P566 H685 V686 E687 K688 N1215 R1216
BS02	rna	A	K351 V516 V520 Q523 R614 Y667 R668 Y671 S1377 K1378 M1379 P1380 Y1620 K1637	K224 V362 V366 Q369 R460 Y513 R514 Y517 S1223 K1224 M1225 P1226 Y1466 K1483
BS03	rna	A	T607 R610 K611 S925 K926 A1322 S1325 K1330 K1334 S1523 R1595 R1650 Y1813 R1818 R1904 L1905 S1906 Q1907	T453 R456 K457 S771 K772 A1168 S1171 K1176 K1180 S1369 R1441 R1496 Y1659 R1664 R1741 L1742 S1743 Q1744
BS04	rna	A	T604 D755 K777 R780 Q784 S787 W790 R791 K794 K846 K847 R851 R854 R928 L929 K1093 D1094 S1325 T1327 M1585 K1588 K1589 R1595 P1602 N1603 P1639 T1640 K1642 K1864 G1868	T450 D601 K623 R626 Q630 S633 W636 R637 K640 K692 K693 R697 R700 R774 L775 K939 D940 S1171 T1173 M1431 K1434 K1435 R1441 P1448 N1449 P1485 T1486 K1488 K1701 G1705
BS05	rna	A	K152 M153 T156 K586 T606 K611 K612 R614 G616 S618 Y725 N728 R732 R737 I741 V742 K743 T746 Q748 R749 Y753	K25 M26 T29 K432 T452 K457 K458 R460 G462 S464 Y571 N574 R578 R583 I587 V588 K589 T592 Q594 R595 Y599

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:5lj3, PDBe:5lj3, PDBj:5lj3
• PDBsum: 5lj3
• PubMed: 27459055
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)