Structure of PDB 6lqp Chain AE

Receptor sequence

>6lqpAE (length=1534) Species: 559292 (Saccharomyces cerevisiae S288C)

SSLSDQLAQVASNNATVALDRKRRQKLHSASLIYNSKTAATQDYDFIFEN
ASKALEELSQIEPKFAIFSRTLFSESSISLDRNVQTKEEIKDLDNAINAY
LLLASSKWYLAPTLHATEWLVRRFQIHVKNTEMLLLSTLNYYQTPVFKRI
LSIIKLPPLFNCLSNFVRSEKPPTALTMIKLFNDMDFLKLYTSYLDQCIK
HNATYTNQLLFTTCCFINVVAFNSNNDEKLNQLVPILLEISAKLLASKSK
DCQIAAHTILVVFATALPLKKTIILAAMETILSNLDAKEAKHSALLTICK
LFQTLKGQGNVDQLPSKIFKLFDSKFDTVSILTFLDKEDKPVCDKFITSY
TRSIARYDRSKLNIILSLLKKIRLERYEVRLIITDLIYLSEILEDKSQLV
ELFEYFISINEDLVLKCLKSLGLTGELFEIRASFQTFLDKHSELINTTNV
SMLTETGERYKKVLSLFTEAIGKGYKASSFLTSFFTTLESRITFLLRVTI
SPAAPTALKLISLNNIAKYINSIEKEVNIFTLVPCLICALRDASIKVRTG
VKKILSLIAKRPSTKHYFLSDKLYGENVTIPMLNPKDSEAWLSGFLNEYV
TENYDISRILTPKRNEKVFLMFWANQALLIPSPYAKTVLLDNLNKSPTYA
SSYSSLFEEFISHYLENRSSWEKSCIANKTNFEHFERSLVNLVSPKEKQS
FMIDFVLSALNSDYEQLANIAAERLISIFASLNNAQKLKIVQNIVDSSSN
VESSYDTVGVLQSLPLDSDIFVSILNQRSSTSKNAFLKEEVALDKVRNVG
SEKGGLPVLYAQETLIYLKEHGCTELTNVRASPQVQNKLLLVIGSLEVIL
HSVMPIFTFMGPALIKNSKGNEKEEMHVPRHRRVKLFSTLVKALGSFLFL
ILVNFKIGEARILIEFHVNEELSGLNDLLDIIKLLTSSKSSSEKKKSLES
RDYYDVRRNLRLKVYSVLDKKLIRNIRVELTFSCITSQENEEASDSETHT
TEIKEILFKVLGNVVDEFVNAVLPLLSTSTNEDIRYHLTLVIGSKFELEG
SEAIPIVNNVMKVLLDRMPLESKSVVISQVILNTMTALVSKYGSILTQAL
TLATEKVSSDMTEVKISSLALITNCVQVLGVKSIAFYPKIVPPSIKLFDA
SLADSSNPLKEQLQVAILLLFAGLIKRIPSFLMSNILDVLHVIYFSREVD
SSIRLSVISLIIENIDLKEVLKVLFRIWSTEIATSNDTVAVSLFLSTLES
TVENIDKKSATSQSPIFFKLLLSLFEFRSISSFDNNTISRIEASVHEISN
SYVLKMNDKVFRPLFVILVRWAFDGEGVTNAGITETERLLAFFKFFNKLQ
ENLRGIITSYFTYLLEPVDMLLKRFISKDMENVNLRRLVINSLTSSLKFD
RDEYWKSTSRFELISVSLVNQLSNIENSIGKYLVKAIGALASNNSGVDEH
NQILNKLIVEHMKASCSSNEKLWAIRAMKLIYSKIGESWLVLLPQLVPVI
AELLEDDDEEIEREVRTGLVKVVENVLGEPFDRY

3D structure

• PDB: 6lqp Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Chain: AE
• Resolution: 3.2 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	AE	R22 Q26 N226	R21 Q25 N225
BS02	rna	AE	K23 R169	K22 R168

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0030515 snoRNA binding
• GO:0034511 U3 snoRNA binding

Biological Process

• 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:0006364 rRNA processing
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis
• GO:0045943 positive regulation of transcription by RNA polymerase I

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005739 mitochondrion
• GO:0030686 90S preribosome
• GO:0030688 preribosome, small subunit precursor
• GO:0032040 small-subunit processome
• GO:0033553 rDNA heterochromatin
• GO:0034455 t-UTP complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lqp, PDBe:6lqp, PDBj:6lqp
• PDBsum: 6lqp
• PubMed: 32943522
• UniProt: P42945|UTP10_YEAST U3 small nucleolar RNA-associated protein 10 (Gene Name=UTP10)