Structure of PDB 6lqv Chain B1

Receptor sequence

>6lqvB1 (length=793) Species: 559292 (Saccharomyces cerevisiae S288C)

KSDFKFSNLLGTVYRQGNITFSDDGKQLLSPVGNRVSVFDLINNKSFTFE
YEHRKNIAAIDLNKQGTLLISIDEDGRAILVNFKARNVLHHFNFKEKCSA
VKFSPDGRLFALASGRFLQIWKTPDVNKDRQFAPFVRHRVHAGHFQDITS
LTWSQDSRFILTTSKDLSAKIWSVDSEEKNLAATTFNGHRDYVMGAFFSH
DQEKIYTVSKDGAVFVWEFTKRKYSWRITKKHFFYANQAKVKCVTFHPAT
RLLAVGFTSGEFRLYDLPDFTLIQQLSMGQNPVNTVSVNQTGEWLAFGSS
KLGQLLVYEWQSESYILKQQGHFDSTNSLAYSPDGSRVVTASEDGKIKVW
DITSGFCLATFEEHTSSVTAVQFAKRGQVMFSSSLDGTVRAWDLIRYRNF
RTFTGTERIQFNCLAVDPSGEVVCAGSLDNFDIHVWSVQTGQLLDALSGH
EGPVSCLSFSQENSVLASASWDKTIRIWSIFGRSQQVEPIEVYSDVLALS
MRPDGKEVAVSTLKGQISIFNIEDAKQVGNIDCRKDIISGRFNQDRFTAK
NSERSKFFTTIHYSFDGMAIVAGGNNNSICLYDVPNEVLLKRFIVSRNMA
LNGTLEFLNSKMRPEVRVTSVQFSPTANAFAAASTEGLLIYSTNDTILFD
PFDLDVDVTPHSTVEALREKQFLNALVMAFRLNEEYLINKVYEAIPIKEI
PLVASNIPAIYLPRILKFIGDFAIESQHIEFNLIWIKALLSASGGYINEH
KYLFSTAMRSIQRFIVRVAKEVVNTTTDNKYTYRFLVSTDGSM

3D structure

• PDB: 6lqv Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Chain: B1
• Resolution: 4.8 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	B1	R563 F569 T570 N573 F629 L630 N631	R541 F547 T548 N551 F607 L608 N609
BS02	rna	B1	R55 R78 H92 F93 N94 K96 W122 F133 A134 P135 F136 R140 H142 A143 W173 S174 S177 K180 M621 N631 S632 K633	R54 R77 H91 F92 N93 K95 W121 F132 A133 P134 F135 R139 H141 A142 W172 S173 S176 K179 M599 N609 S610 K611
BS03	rna	B1	K397 D415 R418 R420 F422 R423 R505	K375 D393 R396 R398 F400 R401 R483
BS04	peptide	B1	F160 Q203 F220	F159 Q202 F219

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:6lqv, PDBe:6lqv, PDBj:6lqv
• PDBsum: 6lqv
• PubMed: 32943522
• UniProt: P25635|PWP2_YEAST Periodic tryptophan protein 2 (Gene Name=PWP2)