Structure of PDB 8ir1 Chain O Binding Site BS01

Receptor Information

>8ir1 Chain O (length=69) Species: 9606 (Homo sapiens)

PRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKE
KAEKLKQSLPPGLAVKELK

Ligand information

>8ir1 Chain 2 (length=3369)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacggcaaaucgguc
guccgaccuggguauaggggcgaaacuaaucaccaucuaguagcugguuc
ccuccgaaguuuccccaggauagcuggcgcucucgcgcaguuuuauccgg
uaaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcg
uggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcug
cgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucag
acccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggcagucgagaguggacgggagcggcggcccggagccccgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaau
auucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaac
agcaguugaacaugggucagucgguccugagagaugggcgagcgccguuc
cgaacgaucgaaagggagucggguucagauccccgaauccggaguggcgg
agaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggaga
agccggcgggagccccggggagaguucucuuuucuuugugaagggcaggg
cgcccuggaauggguucgccccgagagaggggcccgugccuuggaaagcg
ucgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccg
ggggagaggguguaaaucucgcgccgggccguacccauauccgcagcagg
ucuccaaggugaacagccucuggcauguuggaacaauguagguaagggaa
gucggcaagccggauccguaacuucgggauaaggauuggcucuaagggcu
guagcagccgacuuagaacuggugcggaccaggggaauccgacuguuuaa
uuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugau
uucaaagugaagaaaucaaugaaggaguaacuaugacucucgguagccaa
augaacgagauucccacugucccuaccuacuauccagcgaaaccacagcc
aagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcu
ugacucuagucuggcacggugaaguuuuuucacugacccggugaggcggc
cgcuccggggacagugccagguggggaguuugagggcgguacaccuguca
aacgguaacgcagguguccuaaggcgagcucagggaggacagaaaccucc
cguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaau
acagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuua
agcaggaggugucagaaaaguuacagggauaggcuuguggcggccaagcg
uucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucau
ugugaagcagaauucaccaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacggcagcgccgcggagccucgguuggccucggauagccgg
ucccccgccgggguccggugcggagugcccuucguccugggaaacggggc
gcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucgu
ggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggg
uuucguacguagcagagcagcucccucgcugcgaucuauugaaagucagc
ccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ir1 Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): P2 R3 R17 D19 K26 K33 K35 R37 S39 R40 Y41 L42 T44
• Binding residue (residue number reindexed from 1): P1 R2 R16 D18 K25 K32 K34 R36 S38 R39 Y40 L41 T43

Gene Ontology

Molecular Function

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

Biological Process

• GO:0001501 skeletal system development
• GO:0001503 ossification
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0007605 sensory perception of sound
• GO:0022618 protein-RNA complex assembly
• GO:0034463 90S preribosome assembly
• GO:0042474 middle ear morphogenesis
• GO:0048318 axial mesoderm development

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0033291 eukaryotic 80S initiation complex
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ir1, PDBe:8ir1, PDBj:8ir1
• PDBsum: 8ir1
• PubMed: 37491604
• UniProt: P63173|RL38_HUMAN Large ribosomal subunit protein eL38 (Gene Name=RPL38)