Structure of PDB 8jdl Chain d Binding Site BS01

Receptor Information

>8jdl Chain d (length=134) Species: 9606 (Homo sapiens)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>8jdl Chain D (length=3512)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgccgggcccgggucuucccggagucggguugcuugggaaugcagcc
caaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccga
uagucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagag
uucaagagggcgugaaaccguuaagagguaaacgggugggguccgcgcag
uccgcccggaggauucaacccggcggcggguccggccgugucggcgggcg
gaucuuucccgggggaccgucccccgaccggcgaccggccgccgccgggc
gcauuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaa
ggcccggcggggaagguggcucgggggcccccgaguguuacagccccccc
ggcagcagcacucgccgaaucccggggccgagggagcgagacccgucgcc
gcgcucuccccccugggggggccgggccaccccucccacggcgcgaccgc
ucggggcggacuguccccagugcgccccgggcgggucgcgccgucgggcc
cggggggccacgcgcgcgucccgggacggcggagcgagcgcacggggucg
gcggcgacgucggcuacccacccgacccgucuugaaacacggaccaagga
gucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgca
augaaggugaaggccggcgcgcucgccggccgaggugggaucccgaggcc
ucuccaguccgccgagggcgcaccaccggcccgucucgcccgccgcgccg
gggagguggagcacgagcgcacguguuaggacccgaaagauggugaacua
ugccugggcagggcgaagccagaggaaacucugguggagguccguagcgg
uccugacgugcaaaucggucguccgaccuggguauaggggcgaaagacua
aucgaaccaucuaguagcugguucccuccgaaguuucccucaggauagcu
ggcgcucucgcagacccgacccgccacgcaguuuuauccgguaaagcgaa
ugauuagaggucuuggggccgaucucaaccuauucucaaacuuuaaaugg
guaagaagcccggcucgcuggcguggagccgggcguggaaugcgagugcc
uagugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaac
gccggguuaaggcgcccgaugccgacgcucaucagaccccagaaaaggug
uugguugauauagacagccgaaucaacuagcccugaaaauggauggcgcu
ggagcgucgggcccauacccggccgucgccggcagucgagaguggacggg
agccccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagc
cuugaagccuagggcgcgggcccggguggagccgccgcaggugcagaucu
uggugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggag
aaggguuccaugugaacagcaguugaacaugggucagucgguccugagag
augggcgagcgccguuccgaagggacgggcgauggccuccguugcccucg
gccgaucgaaagggagucggguucagauccccgaauccggaguggcggag
augggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaag
ccggcgggagccccggggagaguucucuuuucuuugugaagggcagggcg
cccuggaauggguucgccccgagagaggggcccgugccuuggaaagcguc
gcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccggg
ggagaggguguaaaucucgcgccgggccguacccauauccgcagcagguc
uccaaggugaacagccucuggcauguuggaacaauguagguaagggaagu
cggcaagccggauccguaacuucgggauaaggauuggcucuaagggcugc
agccgacuuagaacuggugcggaccaggggaauccgacuguuuaauuaaa
acaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuucug
cccagugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaa
cggcgggaguaacuaugacucucuuaagguagccaaaugccucgucaucu
aauuagugacgcgcaugaauggaugaacgagauucccacugucccuaccu
acuauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcgg
ggaaagaagacccuguugagcuugacucuagucuggcacggugaagagac
guuuuuucacugacccggugaggcgggggggcgagcucucgcuucuggcg
ccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacagu
gccagguggggaguuugacuggggcgguacaccugucaaacgguaacgca
gguguccuaaggcgagcucagggaggacagaaaccucccguggagcagaa
gggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgugaa
agcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggugu
cagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucaua
gcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugugaa
gcagaauucaccaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaugu
guuguugccaugguaauccugcucaguacgagaggaaccgcagguucaga
cauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccauc
ugugggauuaugacugaacgccucuaagucagaaucccgcccaggcggaa
cgauacggcagcgccgcggagccucgguuggccucggauagccggucccc
ccgggguccggugcggagugcccuucguccugggaaacggggcgcggccg
gagaggcggccgcccccucgcccgucacgcaccgcacguucguggggaac
cuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgua
cguagcagagcagcucccucgcugcgaucuauugaaagucagcccucgac
acaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jdl Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
• Resolution: 2.42 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 T8 S9 R11 K13 N14 R15 H18 K28 P33 K36 R39 R45 S46 R59 G60 H61 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 K132
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 T8 S9 R11 K13 N14 R15 H18 K28 P33 K36 R39 R45 S46 R59 G60 H61 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 K132

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdl, PDBe:8jdl, PDBj:8jdl
• PDBsum: 8jdl
• PubMed: 37992713
• UniProt: P61254|RL26_HUMAN Large ribosomal subunit protein uL24 (Gene Name=RPL26)