Structure of PDB 8y0u Chain SJ Binding Site BS01

Receptor Information

>8y0u Chain SJ (length=184) Species: 4932 (Saccharomyces cerevisiae)

PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSK
IRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKV
EDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLD
SEKHIDFAPTSPFGGARPGRVARRNAARKAEASG

Ligand information

>8y0u Chain C2 (length=1771)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggccggucggauuuccaacggggccuuuccuucuggcuaaccuugagcuu
ggcgaaccaggacuuuuacuuugaaaaaauuagaguguucaaagcaggcg
uauugcucgaauauauuagcauggaauaauagaauaggacguuugguucu
auuuuguugguuucuaggaccaucguaaugauuaauagggacggucgggg
gcaucaguauucaauugucagaggugaaauucuuggauuuauugaagacu
aacuacugcgaaagcauuugccaaggacguuuucauuaaucaagaacgaa
aguuaggggaucgaagaugaucagauaccgucguagucuuaaccauaaac
uaugccgacuagggaucgggugguguuuuuuuaaugacccacucggcacc
uuacgagaaaucaaagucuuuggguucuggggggaguauggucgcaaggc
ugaaacuuaaaggaauugacggaagggcaccaccaggaguggagccugcg
gcuuaauuugacucaacacggggaaacucaccagguccagacacaauaag
gauugacagauugagagcucuuucuugauuuugugggugguggugcaugg
ccguucuuaguugguggagugauuugucugcuuaauugcgauaacgaacg
agaccuuaaccuacuaaauaguggugcuagcauuugcugguuauccacuu
cuuagagggacuaucgguuucaagccgauggaaguuugaggcaauaacag
gucugugaugcccuuagacguucugggccgcacgcgcgcuacacugacgg
agccagcgagucuaaccuuggccgagaggucuugguaaucuugugaaacu
ccgucgugcuggggauagagcauuguaauuauugcucuucaacgaggaau
uccuaguaagcgcaagucaucagcuugcguugauuacgucccugcccuuu
guacacaccgcccgucgcuaguaccgauugaauggcuuagugaggccuca
ggaucugcuuagagaagggggcaacuccaucucagagcggagaauuugga
caaacuuggucauuuagaggaacuaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucauu

...<<<<<.{.[[[[>>>>><<<<.<<<<<<...<.<...<......<<<
.<<<..<<....<<....<<..........>>...>>.>>......<<..
......<<<..<<..<<....<<<..................<<....<<
.<<<.....>>>.>>.....>>.........<<<<<..<<....>>..>>
>>><...<<<<<<......(((((((.<<......>>.............
.>>>>>>.....>...<<<<..<<.......>>.>>>>....>>>...>>
>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>..
....>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<.......
...>>>.>>.<.<<....>>.>...>>>>>>.........<<<....<<<
.....>>>..>>>..>....>.>.....<<<<<<<<<<<<<....>>>>>
>>>>>.>>>......<<..<...........>..>>.........<<<<<
((......<<<<.....<<..))>>.......>>>>.>>>>>..>>>>>>
>>>>.........<<<[[.....<.<<...<<<.<<....<<<<<<.<<<
<<...........>.>>>>.>>>>>>.....<<<<<..............
......>>>>>....<<<<<.<<.......<<...<.......>..<<<.
....>>>....>>......>>.>>..>>>.........<<<..<<<<<<<
<.....))))))).>>>>>>>>.>>>.....>>....<<<<<<.<<...<
<<<..<<..<<<<<<.<...<<<......>>>......>.>>>>>>..>>
.......<<....>>...>>>>...>>>>>.>>>...>>>...>>.>...
.<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>.......
...<<<.<<.<<<..<<<<<<<<.<<<........>>>>>>>>>>>..>>
>...<<..]]>>...>>.....>>>.>>>.<<<......<<<<....>>>
>....>>>..]]]].}<<<<<.<<<<<<<..<<.<<<<<<..<<<.<<<<
<<......<<........>>..........<<<<<.<....<<<<<....
....<<.<<<........>>>.>>......>>>>>...<<.<<<..<<.<
<<<<<....<<<.<.<<......>>...<<<......>>>....>.>>>.
...<<<<<.<<..<<<<..<<<<<.<<<<<<....>>>>>>...>>>>>.
.>>>>.>>....<<<<<<.....>>>>>>.......>>>>>....>>>.>
>>.....>>>>>>>.....>.>>>>>...>>.>>>>.>>>.....<<<<<
<<......<<.....<<..<<<<....>>>>..>>....>>.......>>
>>>>>......<....<<<<<<..........>>>>>>....>.....>>
>>>>....<<<<<<<<.......>>>>>>>>......>>...>>>>>>>>
>>.>>....<..<<.<..<<<<.<<....<<<<<<<<.<<<..<.<<..<
...<<<<<<<.<<<................>>>.>>>>>>>...>..>>.
>..>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<
....>>>>>>>>>........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0u dormant ribosome with STM1
• Resolution: 3.59 Å
• Binding residue (original residue number in PDB): P2 R3 P5 R6 T7 Y8 S9 K10 T11 T14 K16 R17 P18 Y19 K37 N38 K39 K40 R44 S50 R53 F71 R79 K120 Q131 R132 H133 N142 I143 S145 F146 R149 P169 G170 V172 A173 R175 N176
• Binding residue (residue number reindexed from 1): P1 R2 P4 R5 T6 Y7 S8 K9 T10 T13 K15 R16 P17 Y18 K36 N37 K38 K39 R43 S49 R52 F70 R78 K119 Q130 R131 H132 N141 I142 S144 F145 R148 P168 G169 V171 A172 R174 N175

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042254 ribosome biogenesis
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:0043226 organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0u, PDBe:8y0u, PDBj:8y0u
• PDBsum: 8y0u
• PubMed: 38698775
• UniProt: O13516|RS9A_YEAST Small ribosomal subunit protein uS4A (Gene Name=RPS9A)