Structure of PDB 8jdl Chain O Binding Site BS01

Receptor Information

>8jdl Chain O (length=206) Species: 9606 (Homo sapiens)

GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLGGH
MVSDEYEQLSSEALEAARICANKYMVKSCGRDGFHMRVRLHPFHVIRINK
MLLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNEEHVIEALRRAKFK
FPGRQKIHISKKWGFTKFNADEFEDMVAKKCLIPDGCGVKYVPSHGPLDK
WRVLHS

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

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

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): R3 R4 A6 R7 K13 K15 Y17 F22 R24 D35 K39 E63 A64 K74 R90 H92 F94 R98 N100 M115 R116 G117 A118 F119 F157 K158 P160 G194 K198
• Binding residue (residue number reindexed from 1): R2 R3 A5 R6 K12 K14 Y16 F21 R23 D34 K38 E62 A63 K73 R89 H91 F93 R97 N99 M107 R108 G109 A110 F111 F149 K150 P152 G186 K190

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation
• GO:0007141 male meiosis I
• GO:0007283 spermatogenesis
• GO:0030154 cell differentiation
• GO:0051321 meiotic cell cycle

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8jdl, PDBe:8jdl, PDBj:8jdl
• PDBsum: 8jdl
• PubMed: 37992713
• UniProt: Q96L21|RL10L_HUMAN Ribosomal protein uL16-like (Gene Name=RPL10L)