Structure of PDB 5nrl Chain A

Receptor sequence

>5nrlA (length=2216) Species: 4932 (Saccharomyces cerevisiae)

YTPKAEMPPEHLRKIINTHSDDKKAFLGALKYLPHAILKLLENMPHPWEQ
AKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRREKRDRTHFK
RMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVKDWLYDSRP
LEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNYYYLFDKKS
FFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRVPIRSEYKV
AFPHLYNSRPRSVRIPWYNNPVSCIIQNDTPALFFDPSLNPIPHFDFTLP
EDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKKW
FLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNTK
YFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKTL
TTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIHY
ILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFWQ
PAWRVWLNFLRGTIPLLERYIGNLITRQFEDAYYDLELRNSVMDDILEMM
PESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIKKIIERYIKSKA
DAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKNEQERQRQIQKN
GPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDTKILVLALEDLK
DVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQRVFKPVDIT
MMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNWIKPSDSEI
PPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKIDFTLLNRLL
RLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASFIFQYYGLV
IDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYTRYLDRIYM
LFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSRMRLIRQDV
NLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSMCGFEVRIL
PRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEIKKFDSRIRGIL
MASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVKGETRIQNR
VKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPASDLSWSKQTDT
GITHFRAGMTHEDEKLIPTIFRYITTWENEFLDSQRVWAEYATKRQEAIQ
QNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYDRGHRIRREFKQYSLE
RNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIETILEHTLFKGTGFNSW
EGLFWEKASGFEDSMQFKKLTHAQRTGLSQIPNRRFTLWWSPTINRANVY
VGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDICQILD
GELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPSLLHET
NDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSP
TGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVLRERIR
KGLQIYQSSVQEPFLNSSNYAELFNNDIKLFVDDTNVYRVTVHKNVATKA
INGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSL
PKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKL
SDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKM
ILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISAL
TQTEIKDIILGQNIKAPSVKRQKMAELEAARSEKQMKTKTINAQGEEIVV
VASADYESQTFSSKNEWRKSAIANTLLYLRLKNIYVSADDFVEEQNVYVL
PKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGS
VQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKK
RDCIDISIFSTPGSVSLSAYNLTDEGYQWGEENKDIMNVLSEGFEPTFST
HAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQEGDYNFKYGIPLEFYNE
MHRPVHFLQFSELAGD

3D structure

• PDB: 5nrl Structure of a pre-catalytic spliceosome.
• Chain: A
• Resolution: 7.2 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	A931 F1587 K1588 K1589 Q2076 A2099 A2103	A761 F1417 K1418 K1419 Q1902 A1925 A1929
BS02	rna	A	K174 E204 T205 R207 R284 G295 T296 S297 K333 K340 L355 F484 K492 R495 Q497 K503 K504 L531 N532 H535 T537 P539 N541 K544 K549 K552 N553 K670 Y671 K672 H675 R709 N713 R716 G717 P720 R836 K1362 R1366 N1369 L1373 M1379	K39 E69 T70 R72 R149 G160 T161 S162 K198 K205 L220 F329 K337 R340 Q342 K348 K349 L376 N377 H380 T382 P384 N386 K389 K394 K397 N398 K515 Y516 K517 H520 R554 N558 R561 G562 P565 R666 K1192 R1196 N1199 L1203 M1209
BS03	rna	A	P515 V516 T607 K611 R614 H659 Q662 Y671 K681 K684 K697 S1377 K1378 F1623 D1628 L1629 G1636 K1637 K1642 I1646 Q1647 R1650 A1651 H1652 R1689	P360 V361 T452 K456 R459 H504 Q507 Y516 K526 K529 K542 S1207 K1208 F1453 D1458 L1459 G1466 K1467 K1472 I1476 Q1477 R1480 A1481 H1482 R1519

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:5nrl, PDBe:5nrl, PDBj:5nrl
• PDBsum: 5nrl
• PubMed: 28530653
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)