Structure of PDB 5mq0 Chain A

Receptor sequence

>5mq0A (length=1914) Species: 4932 (Saccharomyces cerevisiae)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPFNSIDRVIFRVPIRSEYKV
AFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPSLEDFAPLL
AEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKKWFLQHPDE
EYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNTKYFQQTTI
DWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKTLTTKERKK
SRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIHYILNHIGQ
LTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFWQPAWRVWL
NFLRGTIPLLERYIGNLITRQFEGRSNEIVKTTTKQRLDAYYDLELRNSV
MDDILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIKKII
ERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKNEQE
RQRQIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDTKIL
VLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQR
VFKPVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNW
IKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKID
FTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASF
IFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYT
RYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSR
MRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSM
CGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEIKKF
DSRIRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVK
GETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPASDL
SWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITTWENEFLDSQRVWAEYA
TKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYDRGHRIRR
EFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIETILEHTLF
KGTGFNSWEGLFWQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHG
KIPTLKISLIQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETV
HPRKSYKMNSSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDV
QLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDA
YGNWFNGLKPLIQNSMRTIMKANPALYVLRERIRKGLQIYQSSVQEPFLN
SSNYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKT
GHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVT
RKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQM
VLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKS
YHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDIILGQ
NIKAPSVKRQKMAE

3D structure

• PDB: 5mq0 Structure of a spliceosome remodelled for exon ligation.
• Chain: A
• Resolution: 4.17 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	T607 K608 K611 Y1858 N1869 V1870 T1872 K1903 R1904 S1906 R1937	T445 K446 K449 Y1672 N1683 V1684 T1686 K1717 R1718 S1720 R1751
BS02	rna	A	K351 V516 V520 Q523 K524 R614 Y667 R668 Y671 R678 S1377 K1378 M1379 P1380 Y1620 V1621 G1636 K1637	K225 V354 V358 Q361 K362 R452 Y505 R506 Y509 R516 S1215 K1216 M1217 P1218 Y1434 V1435 G1450 K1451
BS03	rna	A	D751 D755 R759 R780 Q784 S787 W790 K794 K819 K846 K847 R851 R854 N930 A931 K1093 D1094 K1864	D589 D593 R597 R618 Q622 S625 W628 K632 K657 K684 K685 R689 R692 N768 A769 K931 D932 K1678
BS04	rna	A	K152 M153 K555 K586 T606 K611 G616 S618 Y725 N728 L729 R732 R737 I741 K743 T744 T746 Q748 R749 A752 Y753 H1863 T1865 E1867 N1869 A1871 K1873 A1900 G1901 K1903	K26 M27 K393 K424 T444 K449 G454 S456 Y563 N566 L567 R570 R575 I579 K581 T582 T584 Q586 R587 A590 Y591 H1677 T1679 E1681 N1683 A1685 K1687 A1714 G1715 K1717
BS05	rna	A	Y128 P130 H170 K174 K190 T205 R207 R284 G295 T296 S297 K299 K300 K325 K333 K334 K340 F352 E353 W402 F484 R495 D498 A500 K503 K527 N528 N532 H535 T537 L538 P539 N541 N543 K549 K552 K670 Y671 K672 H675 Q676 R709 N713 R716 G717 P720 K747 H839 V840 E841 K842 R1366 N1369 R1370	Y2 P4 H44 K48 K64 T79 R81 R158 G169 T170 S171 K173 K174 K199 K207 K208 K214 F226 E227 W267 F322 R333 D336 A338 K341 K365 N366 N370 H373 T375 L376 P377 N379 N381 K387 K390 K508 Y509 K510 H513 Q514 R547 N551 R554 G555 P558 K585 H677 V678 E679 K680 R1204 N1207 R1208
BS06	IHP	A	K517 H659 K684 H685 Y688 Y689 K697 G698	K355 H497 K522 H523 Y526 Y527 K535 G536

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:5mq0, PDBe:5mq0, PDBj:5mq0
• PDBsum: 5mq0
• PubMed: 28076345
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)