Structure of PDB 5wlc Chain LO

Receptor sequence

>5wlcLO (length=834) Species: 1247190 (Saccharomyces cerevisiae BY4741)

KSDFKFSNLLGTVYRQGNITFSDDGKQLLSPVGNRVSVFDLINNKSFTFE
YEHRKNIAAIDLNKQGTLLISIDEDGRAILVNFKARNVLHHFNFKEKCSA
VKFSPDGRLFALASGRFLQIWKTPDVNKDRQFAPFVRHRVHAGHFQDITS
LTWSQDSRFILTTSKDLSAKIWSVDSEEKNLAATTFNGHRDYVMGAFFSH
DQEKIYTVSKDGAVFVWEFTKRKYSWRITKKHFFYANQAKVKCVTFHPAT
RLLAVGFTSGEFRLYDLPDFTLIQQLSMGQNPVNTVSVNQTGEWLAFGSS
KLGQLLVYEWQSESYILKQQGHFDSTNSLAYSPDGSRVVTASEDGKIKVW
DITSGFCLATFEEHTSSVTAVQFAKRGQVMFSSSLDGTVRAWDLIRYRNF
RTFTGTERIQFNCLAVDPSGEVVCAGSLDNFDIHVWSVQTGQLLDALSGH
EGPVSCLSFSQENSVLASASWDKTIRIWSIFGRSQQVEPIEVYSDVLALS
MRPDGKEVAVSTLKGQISIFNIEDAKQVGNIDCRKDIISGRFNQDRFTAK
NSERSKFFTTIHYSFDGMAIVAGGNNNSICLYDVPNEVLLKRFIVSRNMA
LNGTLEFLNSKKMTEAGSLDLIDDAGENSDLEDRIDNSLPGSQRGGDLST
RKMRPEVRVTSVQFSPTANAFAAASTEGLLIYSTNDTILFDPFDLDVDVT
PHSTVEALREKQFLNALVMAFRLNEEYLINKVYEAIPIKEIPLVASNIPA
IYLPRILKFIGDFAIESQHIEFNLIWIKALLSASGGYINEHKYLFSTAMR
SIQRFIVRVAKEVVNTTTDNKYTYRFLVSTDGSM

3D structure

• PDB: 5wlc The complete structure of the small-subunit processome.
• Chain: LO
• 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	LO	R78 H92 F93 N94 F118 W122 F133 A134 P135 F136 R140 H142 A143 W173 S174 D176 S177 K180 N188 R191 D212 W218 S247 W248 R249 I250 F255 Y257 Q260 N631 L653	R77 H91 F92 N93 F117 W121 F132 A133 P134 F135 R139 H141 A142 W172 S173 D175 S176 K179 N187 R190 D211 W217 S225 W226 R227 I228 F233 Y235 Q238 N609 L631
BS02	rna	LO	K397 Q400 D415 R418 R420 N421 F422 R423 Q461 R505 S506	K375 Q378 D393 R396 R398 N399 F400 R401 Q439 R483 S484
BS03	rna	LO	R563 R568 T570 N573 F629 L630 N631	R541 R546 T548 N551 F607 L608 N609

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0005515 protein binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000920 septum digestion after cytokinesis
• GO:0006364 rRNA processing
• GO:0030010 establishment of cell polarity
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:0034388 Pwp2p-containing subcomplex of 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5wlc, PDBe:5wlc, PDBj:5wlc
• PDBsum: 5wlc
• PubMed: 28945246
• UniProt: P25635|PWP2_YEAST Periodic tryptophan protein 2 (Gene Name=PWP2)