Structure of PDB 6lqs Chain B3 Binding Site BS01

Receptor Information

>6lqs Chain B3 (length=757) Species: 559292 (Saccharomyces cerevisiae S288C)

LKTSYKGISLNPIYAGSSAVATVSENGKILATPVLDEINIIDLTPGSRKI
LHEITALKLTPDGQYLTYVSQAQLLKIFHLKTGKVVRSMKISSPSYILDA
DSTSTLLAVGGTDGSIIVVDIENGYITHSFKGHGGTISSLKFYGQLNSKI
WLLASGDTNGMVKVWDLVKRKCLHTLQEHTSAVRGLDIIEVPPSLNLLSG
GRDDIINLWDFNMKKKCKLLKTLPVNQQVESCGFLKIIYTAGGDAIFQLI
DSESGSVLKRTNKPIEELFIIGVLPILSNSQMFLVLSDQTLQLINVEEDL
KNTIQVTSSIAGNHGIIADMRYVGPELNKLALATNSPSLRIIPVPDLASL
PLDVEIYEGHEDLLNSLDATEDGLWIATASKDNTAIVWRYKFDIYAKYIG
HSAAVTAVGLPNIVSKGYPEFLLTASNDLTIKKWIIPKPTASMDVQIIKV
SEYTINALSVSPNDSIFATASYDKTCKIWNLENGELEATLANHKRGLWDV
SFCQYLLATSSGDKTVKIWSSVMKTLEGHTNAVQRCSFINKQKQLISCGA
DGLIKCLKTLDGHNNRLWALSTMNDGDMIVSADADGVFQFWKDCTEQEIE
EEQEKAKLQVEQEQSLQNYMSKGDWTNAFLLAMTLDHPMRLFNVLKRALG
ESRSRQEVIFNEELDQAISILNDEQLILLMKRCRDWNTNAKTHTIAQRTI
RCILMHHNIAKLSEIPGMVKIVDAIIPYTQRHFTRVDNLVEQSYILDYAL
VEMDKLF

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): K408 N749 A750 K751 R791 R795
• Binding residue (residue number reindexed from 1): K381 N689 A690 K691 R731 R735

Gene Ontology

Molecular Function

• GO:0005515 protein 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

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• 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:6lqs, PDBe:6lqs, PDBj:6lqs
• PDBsum: 6lqs
• PubMed: 32943522
• UniProt: Q05946|UTP13_YEAST U3 small nucleolar RNA-associated protein 13 (Gene Name=UTP13)