Structure of PDB 8y0w Chain SI Binding Site BS01

Receptor Information

>8y0w Chain SI (length=206) Species: 9606 (Homo sapiens)

GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDE
RKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
IKARKG

Ligand information

>8y0w Chain L5 (length=3666)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggccggagccccgcggacgcuacgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggagccgccgcagg
ugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggcc
gaaguggagaaggguuccaugugaacagcaguugaacaugggucagucgg
uccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccg
uugcccucggccgaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgcggccggcgccuagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagugaucguuuuuuc
acugacccggugaggcgggggggcgagccccgaggggcucucgcuucugg
cgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggaca
gugccagguggggaguuugacuggggcgguacaccugucaaacgguaacg
cagguguccuaaggcgagcucagggaggacagaaaccucccguggagcag
aagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgug
aaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggu
gucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguuca
uagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugug
aagcagaauucaccaagcguuggauuguucacccacuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugau
guguuguugccaugguaauccugcucaguacgagaggaaccgcagguuca
gacauuugguguaugugcuuggcugaggagccaauggggcgaagcuacca
ucugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgg
aacgauacggcagcgccgcggagccucgguuggccucggauagccggucc
cccgccgggguccggugcggagugcccuucguccugggaaacggggcgcg
gccggagaggcggccgcccccucgcccgucacgcaccgcacguucguggg
gaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuu
cguacguagcagagcagcucccucgcugcgaucuauugaaagucagcccu
cgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y0w dormant ribosome with eIF5A, eEF2 and SERBP1
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R92 K124 Q168 K170 K206
• Binding residue (residue number reindexed from 1): R91 K123 Q167 K169 K205

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
• PDBsum: 8y0w
• PubMed: 38698775
• UniProt: P62241|RS8_HUMAN Small ribosomal subunit protein eS8 (Gene Name=RPS8)