Structure of PDB 3jcm Chain A Binding Site BS01

Receptor Information

>3jcm Chain A (length=2174) Species: 559292 (Saccharomyces cerevisiae S288C)

PKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLLENM
PHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRREKR
DRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVKDW
LYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNYYY
LFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRVPI
RSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPSLN
PIGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQ
DVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKL
LKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNF
NLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAF
QLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGK
GPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRLDAYYDLELR
NSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIK
KIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKN
EQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDT
KILVLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLL
TQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLF
PNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAE
KIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKF
ASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIR
LYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPK
DSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLL
FSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEI
KKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDI
LVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPA
SDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITTWENEFLDSQRVWA
EYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYDRGHR
IRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIETILEH
TLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQRTGLSQIPNRRFTLW
WSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHE
SIVFDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEW
EVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDY
TTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKAN
PALYVLRERIRKGLQIYQSSVQEPFLNSSNYAELFNNDIKLFVDDTNVYR
VTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLA
KWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPT
ELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLT
LLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLI
LTEYGRKYNVNISALTQTEIKDIILGSKNEWRKSAIANTLLYLRLKNIYV
SADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEI
KTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAA
SEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTDEGYQWGEENKDI
MNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQEGD
YNFKYGIPLEFYNEMHRPVHFLQF

Ligand information

>3jcm Chain C (length=20)

aaaaaauuaagguauguauu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3jcm The 3.8 angstrom structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K611 R614 R668 Y671 R678 S1377 K1378 G1622 F1623 V1625 H1635 G1636 K1637
• Binding residue (residue number reindexed from 1): K464 R467 R521 Y524 R531 S1218 K1219 G1463 F1464 V1466 H1476 G1477 K1478

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:3jcm, PDBe:3jcm, PDBj:3jcm
• PDBsum: 3jcm
• PubMed: 26743623
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)