Structure of PDB 6zqb Chain UT

Receptor sequence

>6zqbUT (length=2234) Species: 559292 (Saccharomyces cerevisiae S288C)

QRQTTKSSKRYRYSSFKARIDDLKIEPARNLEKRVHDYVESSHFLASFDQ
WKEINLSAKFTEFAAEIEHDVQTLPQILYHDKKIFNSLVSFINFHDEFSL
QPLLDLLAQFCHDLGPDFLKFYEEAIKTLINLLDAAIEFESSNVFEWGFN
CLAYIFKYLSKFLVKKLVLTCDLLIPLLSHSKEYLSRFSAEALSFLVRKC
PVSNLREFVRSVFEKLEGDDEQTNLYEGLLILFTESMTSTQETLHSKAKA
IMSVLLHEALTKSSPERSVSLLSDIWMNISKYASIESLLPVYEVMYQDFN
DSLDATNIDRILKVLTTIVFSESGRKIPDWNKITILIERIMSQSEQDKVA
FLFALFIRNSDVKTLTLFHQKLFNYALTNISDCFLEFFQFALRLSYERVF
SFNGLKFLQLFLKKNWQSQGKKIALFFLEVDDKPELQKVREVNFPEEFIL
SIRDFFVTAEINDSNDLFEIYWRAIIFKYSKLQNTEIIIPLLERIFSTFA
SPDNFTKDMVGTLLKIYRKNNLLKTILDNYENYKESLNFLRGWNKLVSNL
HPSESLKGLMSHYPSLLLSLTDNFMLPDGKIRYETLELMKTLMILQGMQV
PDLLSSCMVIEEIPLTLQNARDLTIRIKNVGAEFGKTKTDKLVSSFFLKY
LFGLLTVRFSPVWTGVFDTLPNVYTKDEALVWKLVLSFIKLPDENQNLDY
YQPLLEDGANKVLWDSSVVRLRDTIDTFSHIWSKYSTQNTSIISTTIERR
GNTTYPILIRNQALKVMLSIPQVAENHFVDIAPFVYNDFSWTEVDRNVFL
KTLSKFKNIKNVYSATELHDHLMVLLGSRNTDVQKLALDALLAYKNPTLN
KYRDNLKNLLDDTLFKDEITTFLTENGSQSIKAEDEKVVMPYVLRIFFGR
AQVPPTSGQKRSRKIAVISVLPNFKKPYINDFLSLASERLDYNYFFGNSH
QINSSKATLKTIRRMTGFVNIVNSTLSVLRTNFPLHTNSVLQPLIYSIAM
AYYVLDTESTEEVHLRKMASNLRQQGLKCLSSVFEFVGNTFDWSTSMEDI
YAVVVKPRISHFSDENLQQPSSLLRLFLYWAHNPSLYQFLYYDEFATATA
LMDTISNQHVKEAVIGPIIEAADSIIRNPVNDDHYVDLVTLICTSCLKIL
PSLYVKDSNSISTFLNLLVSITEMGFIQDDHVRSRLISSLISILKGKLKK
LQENDTQKILKILKLIVFNYNCSWSDIEELYTTISSLFKTFDERNLRVSL
TELFIELGRKVPELESISKLVADLNSYSSSRMHEYDFPRILSTFKGLIED
GYKSYSELEWLPLLFTFLHFINNKEELALRTNASHAIMKFIDFINEKPNL
NEASKSISMLKDILLPNIRIGLRDSLEEVQSEYVSVLSYMVKNTKYFTDF
EDMAILLQLHRRQRAIKRLGEHAHQLKDNSISHYLIPMIEHYVFSRNIGN
ETQIAIGGLAQHMSWNQYKALLRRYISMLKTKPNQMKQAVQLIVQLSVPL
RETLRIVRNFIKQELYPTLSKILGTRDDETIIERMPIAEALVNIVLGLTN
DDITNFLPSILTNICQVLRSKSEELRDAVRVTLGKISIILGAEYLVFVIK
ELMATLKRGSQIHVLSYTVHYILKSMHGVLKHSDLDTSSSMIVKIIMENI
FGFAGEEKDSENYHTKVKEIKSNKSYDAGEILASNISLTEFGTLLSPVKA
LLMVRINLRNQNKLSELLRRYLLGLNHNSDSESESILKFCHQLFQESEMS
ENSTLQKFALDLLRNVITRHRSFLTVSHLEGFIPFLRDSLLSNEGVVIST
LRILITLIRLDFSDESSEIFKNCARKVLNIIKVSPSTSSELCQMGLKFLS
AFIRHTDSTLKDTALSYVLGRVLPDLNEPSRQGLAFNFLKALVSKHIMLP
ELYDIADTTREIMVTNHSKEIRDVSRSVYYQFLMEYDQSKGRLEKQFKFM
VDNLQYPTESGRQSVMELINLIITKANPALLSKLSSSFFLALVNVSFNDD
APRCREMASVLISTMLPKLENKDLEIVEKYIAAWLNASFLNLGLRTYKVY
LKSEHTIELDELAIKRIRYILSDTQWDLVYSALNTFSSYMEATGFKDIWD
GIITCLLYHSWVRQSAANLVHQLIANKNLEIQTIATRILHQLGAPENLAN
VSIKTLVNISILWKEQRIDYMVTRIGGIIRSSFMSKKACIQLLALLVQVE
DEVIAEEKILLPLYGYEELRTLSNECLKILEDKL

3D structure

• PDB: 6zqb 90 S pre-ribosome transformation into the primordial 40 S subunit.
• Chain: UT
• Resolution: 3.9 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	UT	Q4 Y16 S939 Q941 E1097 N1521 A1525 R1528 R1529 T1740	Q1 Y13 S907 Q909 E1065 N1466 A1470 R1473 R1474 T1665

Gene Ontology

Molecular Function

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

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0030686 90S preribosome
• GO:0030688 preribosome, small subunit precursor
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6zqb, PDBe:6zqb, PDBj:6zqb
• PDBsum: 6zqb
• PubMed: 32943521
• UniProt: P35194|UTP20_YEAST U3 small nucleolar RNA-associated protein 20 (Gene Name=UTP20)