Structure of PDB 6lqs Chain RP Binding Site BS01

Receptor Information

>6lqs Chain RP (length=2180) Species: 559292 (Saccharomyces cerevisiae S288C)

KRYRYSSFKARIDDLKIEPARNLEKRVHDYVESSHFLASFDQWKEINLSA
KFTEFAAEIEHDVQTLPQILYHDKKIFNSLVSFINFHDEFSLQPLLDLLA
QFCHDLGPDFLKFYEEAIKTLINLLDAAIEFESSNVFEWGFNCLAYIFKY
LSKFLVKKLVLTCDLLIPLLSHSKEYLSRFSAEALSFLVRKCPVSNLREF
VRSVFEKLELYEGLLILFTESMTSTQETLHSKAKAIMSVLLHEALTKSSP
ERSVSLLSDIWMNISKYASIESLLPVYEVMYQDFNDSRILKVLTTIVFSE
IPDWNKITILIERIMLSQDKVAFLFALFIRNSDVKTLTLFHQKLFNYALT
NISDCFLEFFQFALRLSYERVFSFLFLKKNWQSQGKKIALFFLEVDDKPE
LQKVREVNFPEEFILSIRDFFVTAEINDSNDLFEIIFKYSKLQNTEIIER
IFSTFASPDNFTKGTLLKIYRKEDDASLKTILDNYENYKESLGWNKLVSN
LHPSESLKGLMSHYPSLLLSLTDNFMLPDGKIRYKTLMILQGMQVPDLLS
SCMVIEEIPLTLQNARDLTIRIKTKTDKLVSSFFLKYLFGLLTVRFSPVW
TGVFDTLPNVYTKDEALVWKLVLSFIKLPDENQNLDYYQPLLEDGANKVL
WDSSVVRLRDTIDTFSHIWSKYSTQNTSIISTTIERRGNTTYPILIRNQA
LKVMLSIPQVAENHFVDIAPFVYNDFKTYKDEEDMENERVITGSWTEVDR
NVFLKTLSKFKNIKNVYSATELHDHLMVLLGSRNTDVQKLALDALLAYKN
PTLNKYRDNLKNLLDDTLFKDEITTFLTENGSQSIKAEDEKVVMPYVLRI
FFGRAQVPPTSGQKRSRKIAVISVLPNFKKPYINDFLSLASERLDYNYFF
GNSHQINSSKATLKTIRRMTGFVNIVNSTLSVLRTNFPLHTNSVLQPLIY
SIAMAYYVLDTESTEEVHLRKMASNLRQQGLKCLSSVFEFVGNTFDWSTS
MEDIYAVVVKPRISHFSDENLQQPSSLLRLFLYWAHNPSLYQFLYYDEFA
TATALMDTISNQHVKEAVIGPIIEAADSIIRNPVNDDHYVDLVTLICTSC
LKILPSLYVKLSDSNSISTFLNLLVSITEMGFIQDDHVRSRLISSLISIL
KGKLKKLQENDTQKILKILKLIVFNYNCSWSDIEELYTTISSLFKTFDER
NLRVSLTELFIELGRKVPELESISKLVADLNSYSSSRMHEYDFPFINEKP
NLNEASKSISMLKDILLPNIRIGLRDSLEEVVLSYMVKNTKYFTDFEDMA
ILLYNGDEEADRRQRAIKRLGEHAHQLKDNSISHYLIPMIEHYVFSDDER
YRNIGNETQIAIGGLAQHMSWNQYKALLRRYISMLKTKPNQMKQAVQLIL
RIVRDGAESKLTLSKFPSDEPSNFIKQELYPTLSKILTNFLPSILTNICQ
VLRSKSEELRDAVRVTLGKISIILGAEYLVFVIKELMATLKRGSQIHVLS
YTVHYILKSMHGVLKHSDLDTSSSMIVKIIMENIFGFAGEEKDSENYHTK
VKEIKSNKSYDAGEILASNISLTEFGTLLSPVKALLMVRINLRNQNKLSE
LLRRYLLGLNHNSDSESESILKFCHQLFQESEKEDFFLVNLESKSYTINS
NSLLLNSTLQKFALDLLRNVITRHRSFLTVSHLEGFIPFLRDSLLSENEG
VVISTLRILITLIRLDFSDESSEIFKNCARKVLNIIKVSPSTSSELCQMG
LKFLSAFIRHTDSTLKDTALSYVLGRVLPDLNEPSRQGLAFNFLKALVSK
HIMLPELYDIADTTREIMVTNHSKEIRDVSRSVYYQFLMEYDQSKGRLEK
QFKFMVDNLQYPTESGRQSVMELINLIITKPALLSKLSSSFFLALVNVSF
NDDAPRCREMASVLISTMLPKLENKDLEIVEKYIAADNASFLNLGLRTYK
VSIGFEHTIELDELAIKRIRYILSDTSVGSEHQWDLVFSSYMEATESVYK
HGWDGIITCLLYPHSWVANLVHQLIANKDKLEISLTTIATRILHQLGAPS
IPANVSIKTLVNISILWKEQTGEDLKYTTAIDYMVTRGIIRSDEHRMDSF
MSKALLVQVLDEDEVIAEGEYLETYYSRAVDEEQEELLEDKLQVSDFTKI
YTAVKQTVLERRKERRSADKKLRKHARSRE

Ligand information

>6lqs Chain SA (length=1249)

aagauaguuaucugguugauccugccaguagucauaugcuugucucaaag
ccaugcaugucuaaguauaagcaauuuauacagugaaacugcgaaucagu
uaucguuuauuugauagcaugguauaacugugguaauucuagagcuaaua
caugcuaaucucgacccuuuggaagagauguauuuauuagagucuucgga
cucuuugaugauucauaauaacuuuucgaaucgcauggccuugugcuggc
gaugguucauucaaauuucugcccuaucaacuuucgaugguaggauagug
gccuaccaugguuucaacggggcaggcgcgcaaauuacccaauccuaauu
cagggagguagugacaauaaauaacgauacagggcccauucgggucuugu
aauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggc
aagucuggugccagcagccgcgguaauuccagcuccaauagcguauauug
cucguaguugaacuuugggcccgguuggccgguccggauuuccaacgggg
ccuuuccuuuuuacuuugaaaaaauuagaguguucaaagcaggcguauug
cucgaauauauuagcauggaauaauagaauagguugguucuauuucuagg
accugauuaauagggacggucgggggcaucaguauucaauugucagaggu
gaaauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaag
gacguuuucauuaaucaagaacguagggaucgggugguguuuuuuuaaug
acccacucggcaccuugggggaguauggucgcaaggcugaaacuuaaagg
aauugacggaagggcaccaccaggaguggagccugcggcucaacacgggg
aaacucaccagguccagacacaauaaggauugacauucuugauuuugugg
gugguggugcauugaugcccuuguucugggcccgcgcgcuacacugacgg
agccagcgaguaacuccgucgugcugacgaggaauuccuaguaagcgcaa
gucaucagcuugcguugauuacgucccugcccuuuguacacaccgcccgu
cgcuaguaccgauugaauggcuuagugaggccucaggaucugcuuagaga
agggggcaacuccaucucagagcggagaauuuggacaaacuuggucauuu
agaggaacuaaaaggguuuccguaggugaaccugcggaaggaucauuaa

..............................<..<<<<<<...<......<
<<.<<<..<<....<<....<<..........>>...>>.>>....<<<.
.<<..<<....<<<.......<<....<<.<<<.....>>>.>>.....>
>......<<<<<..<<....>>..>>>>><...<<<<<<..<<<<..>>>
>....<<......>>>>>>>>.....>...<<<<..<<<.....>>>.>>
>>....>>>...>>>>..>>>..<<....<<.....<<<<<<<<......
.>>>>>>>>.>>......>>.>>>>>>.........<<<....<<<....
.>>>..>>>.........>.....<<<<<<<..<<<<....>>>>..>>>
>.>>>......<<..<...........>..>>.........<<<<<<...
....<<<....>>>..................>>>>>>..>>>>>>.>.<
.<<...<<<.<<.....<<<<<.<<<<<..<.<...>.>..>>>>>.>>>
>>........<<<<<.<<............<.......>...<<.....>
>.............>>.>>..>>>..........<..<...<..>..>..
>.....>>....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<..
....>>>......>.>>>>>>..>>.......<<....>>...>>>>..>
.>>>>.>>>...>>>...>>.>..<<<..<<<<<<<<.<<<........>
>>>>>>>>>>..>>>.....................<<.........>>.
....<<<<<<<<<<<<..<<.<<<<<<..<<<.<<<<.............
.........<<<......<<<<<.....................>>>>>.
......<<........>>......>>>.....>>>>.>>>.....<<<<<
<<...........>>>>>>>.............>>>>>>....<<<<<<<
<.......>>>>>>>>......>>...>>>>>>>............>>>>
>..<<<<.<<....<.<<<<.<..<<..<.<<......<<...<<.....
.<<<<....>>>>......>>...>>......>>.>..>>..>.>>>>>.
...>>.>>>>.......<<<<<<<<<....>>>>>>>>>..........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lqs Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): Y14 R15 Y16 K20 T906 L1017 C1061 L1062 S1063 I1687 H1688 H1739 S1750 R1794 R1795 L1798 H1802 R1882 K2033
• Binding residue (residue number reindexed from 1): Y3 R4 Y5 K9 T828 L939 C983 L984 S985 I1496 H1497 H1548 S1559 R1603 R1604 L1607 H1611 R1673 K1824

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:6lqs, PDBe:6lqs, PDBj:6lqs
• PDBsum: 6lqs
• PubMed: 32943522
• UniProt: P35194|UTP20_YEAST U3 small nucleolar RNA-associated protein 20 (Gene Name=UTP20)