Structure of PDB 8y0x Chain SJ Binding Site BS01

Receptor Information

>8y0x Chain SJ (length=185) Species: 9606 (Homo sapiens)

PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLA
KIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLK
IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRL
DSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAG

Ligand information

>8y0x Chain S2 (length=1739)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuuaacgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgcccuc
ucggccggggcccgaagcguuuacuuugaaaaaauuagaguguucaaagc
aggcccgagccgccuggauaccgcagcuaggaauaauggaauagaccgcg
guucuauuuuguugguuuucggaacugaggccaugauuaagagggacggc
cgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcgca
agacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaaga
acgaaagucggagguucgaagacgaucagauaccgucguaguuccgacca
uaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgccgg
gcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguugc
aaagcugaaacuuaaaggaauugacggaagggcaccaccaggaguggagc
cugcggcuuaauuugacucaacacgggaaaccucacccggcccggacacg
gacaggauugacagauugauagcucuuucucgauuccgugggugguggug
cauggccguucuuaguugguggagcgauuugucugguuaauuccgauaac
gaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucggc
gucccccaacuucuuagagggacaaguggcguucagccacccgagauuga
gcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcgcu
acacugacuggcucagcgugugccuacccuacgccggcaggcgcggguaa
cccguugaaccccauucgugauggggaucggggauugcaauuauucccca
ugaacgaggaauucccaguaagugcgggucauaagcuugcguugauuaag
ucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguuu
agugaggcccucggaucggccccgccggggucggcccacggcccuggcgg
agcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagucgu
aacaagguuuccguaggugaaccugcggaaggaucauua

...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<..................<<.....
<<.<<<.....>>>.>>......>>.........<<<<...<<<<.....
...>>>>...>>>><<..<<<<<...<......>..>>>>>......>>.
..<<<<.<<<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<<..>>>.>...>>>>>>.........<<<....<<<<...>>>>..>>>
..>...>>.>.....<<.....<<..<<....>>..>>.......>>...
...<<..<...........>..>>.........<<<<<((....<.<<<<
.....<<..))>>.......>>>>>>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<.<<.......................<<.
<.............>>>...<<<<<<.<.......<<...<.......>.
<<<<.......>>>>...>>......>.>>>..>>>.......<.<<.<<
<.<<<...............>>>.>>>.>>.>....>>....<<<<<<..
<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>>>>
>..>>.......<<....>>...>>>>..>..>>>.>>>...>>>...>>
.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>..
........<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>>>.
>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<<..
..>>>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..<<<
.<<<<<<......<<........>>..........<<<<<.<....<<<<
<<.......<<.<<<........>>>.>>.....>>>>>>...<<.<<<.
.<<.<<<<<<....<<<.<<<<<....>>>...<<<......>>>...>>
.>>>....<<<...<...<<<<..<<<<<<<<<<<<.......>>>>.>>
>>.....>>>>..>>>>..>.....<<<<<.....>>>>>........>>
>....>>>.>>>.....>>>>>>>.....>.>>>>>...>>.>>>>.>>>
.....<<.<<<........<.......<<<.<<<<....>>>>.>>>...
.>.........>>>.>>............<<<<<..........>>>>>.
..........>>>>>.....<<<<<<<<.......>>>>>>>>......>
>...>>>>>>>>>>.>>....<..<<....<<<<.<<....<<<<<<<<.
<<<..<<<<.<<...<<<<<...<<.....................>>..
...>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>.....>>.
..>.....<<<<<<<<<<..>>>>>>>>>>.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0x The global structure of dormant ribosome
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): P2 V3 A4 R5 W7 V8 C9 R10 K11 T12 T15 R17 R18 F20 R38 N39 K40 R41 R45 E73 R79 R80 K121 S122 H125 R127 Q132 R133 H134 Q140 V142 I144 S146 F147 I148 R150 R162 P164 R169 G171 R172 V173 K174 K176 N177
• Binding residue (residue number reindexed from 1): P1 V2 A3 R4 W6 V7 C8 R9 K10 T11 T14 R16 R17 F19 R37 N38 K39 R40 R44 E72 R78 R79 K120 S121 H124 R126 Q131 R132 H133 Q139 V141 I143 S145 F146 I147 R149 R161 P163 R168 G170 R171 V172 K173 K175 N176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0045182 translation regulator activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0008284 positive regulation of cell population proliferation
• 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:0005925 focal adhesion
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0043226 organelle
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0x, PDBe:8y0x, PDBj:8y0x
• PDBsum: 8y0x
• PubMed: 38698775
• UniProt: P46781|RS9_HUMAN Small ribosomal subunit protein uS4 (Gene Name=RPS9)