Structure of PDB 6lqt Chain SO Binding Site BS01

Receptor Information

>6lqt Chain SO (length=134) Species: 559292 (Saccharomyces cerevisiae S288C)

KGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAH
GVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKD
KDAKFRLILIESRIHRLARYYRTVAVLPPNWKYE

Ligand information

>6lqt Chain SA (length=1155)

aagauaguuaucugguugauccugccaguagucauaugcuugucucaaag
ccaugcaugucuaaguauaagcaauuuauacagugaaacugcgaaucagu
uaucguuuauuugauagcaugguauaacugugguaauucuagagcuaaua
caugcuaaucucgacccuuuggaagagauguauuuauuagagucuucgga
cucuuugaugauucauaauaacuuuucgaaucgcauggccuugugcuggc
gaugguucauucaaauuucugcccuaucaacuuucgaugguaggauagug
gccuaccaugguuucaacggggcaggcgcgcaaauuacccaauccuaauu
cagggagguagugacaauaaauaacgauacagggcccauucgggucuugu
aauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggc
aagucuggugccagcagccgcgguaauuccagcuccaauagcguauauug
cucguaguugaacuuugggcccgguuggccgguccggauuuccaacgggg
ccuuuccuuuuuacuuugaaaaaauuagaguguucaaagcaggcguauug
cucgaauauauuagcauggaauaauagaauagguugguucuauuucuagg
accugauuaauagggacggucgggggcaucaguauucaauugucagaggu
gaaauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaag
gacguuuucauuaaucaagaacguagggaucgggugguguuuuuuuaaug
acccacucggcaccuugggggaguauggucgcaaggcugaaacuuaaagg
aauugacggaagggcaccaccaggaguggagccugcggcgcgcgcuacac
ugacggagccagcgaguaacuccgucgugcugacgaggaauuccuaguaa
gcgcaagucaucagcuugcguugauuacgucccugcccuuuguacacacc
gcccgucgcuaguaccgauugaauggcuuagugaggccucaggaucugcu
uagagaagggggcaacuccaucucagagcggagaauuuggacaaacuugg
ucauuuagaggaacuaaaaggguuuccguaggugaaccugcggaaggauc
auuaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lqt Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Resolution: 4.9 Å
• Binding residue (original residue number in PDB): K9 I11 S12 S14 A15 I16 P17 R20 S48 Q49 R55 T61 R64 K70 I71 M72 R73 D87 Y90 K94 H101 N105 K107 D108 K109 K112 F113 R114 I116 S120 R121 R124 R127 Y128
• Binding residue (residue number reindexed from 1): K1 I3 S4 S6 A7 I8 P9 R12 S40 Q41 R47 T53 R56 K62 I63 M64 R65 D79 Y82 K86 H93 N97 K99 D100 K101 K104 F105 R106 I108 S112 R113 R116 R119 Y120

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lqt, PDBe:6lqt, PDBj:6lqt
• PDBsum: 6lqt
• PubMed: 32943522
• UniProt: P05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)