Structure of PDB 5lj3 Chain A Binding Site BS02

Receptor Information

>5lj3 Chain A (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

Ligand information

>5lj3 Chain E (length=16)

uaagugaucuagaaag

................

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lj3 Cryo-EM structure of the spliceosome immediately after branching.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K351 V516 V520 Q523 R614 Y667 R668 Y671 S1377 K1378 M1379 P1380 Y1620 K1637
• Binding residue (residue number reindexed from 1): K224 V362 V366 Q369 R460 Y513 R514 Y517 S1223 K1224 M1225 P1226 Y1466 K1483

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)