Structure of PDB 3jcm Chain A

Receptor sequence

>3jcmA (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

3D structure

• PDB: 3jcm The 3.8 angstrom structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis
• 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	K611 R614 R668 Y671 R678 S1377 K1378 G1622 F1623 V1625 H1635 G1636 K1637	K464 R467 R521 Y524 R531 S1218 K1219 G1463 F1464 V1466 H1476 G1477 K1478
BS02	rna	A	K612 D1628 Q1647 R1650 A1651 H1652 R1689	K465 D1469 Q1488 R1491 A1492 H1493 R1530
BS03	rna	A	A931 F1587	A772 F1428
BS04	rna	A	R284 N294 T296 S297 K299 K340 F352 E353 L355 F484 R495 D498 K503 K527 N532 H535 P536 P539 K546 K549 N617 K670 Y671 K672 H675 R716 G717 H839 L1373 K1378	R155 N165 T167 S168 K170 K211 F223 E224 L226 F337 R348 D351 K356 K380 N385 H388 P389 P392 K399 K402 N470 K523 Y524 K525 H528 R569 G570 H680 L1214 K1219

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)