Structure of PDB 8ie3 Chain h Binding Site BS02

Receptor Information

>8ie3 Chain h (length=134) Species: 9606 (Homo sapiens)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>8ie3 Chain 2 (length=3519)

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
cgacgcccgccacgcaguuuuauccgguaaaacuuuaaauggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaacagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggucggucgcggccggcgccuagcagccgacuuagaacugg
ugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaagg
cccgcggcggguguugacgcgaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaugaagcgcggguaaacggcaagaugaacgaga
uucccacugucccuaccuacuauccagcgaaaccacagccaagggaacgg
gcuuggcggaaucagcggggaaagaagacccuguugagcuugacucuagu
cuggcacggugaaguuuuuucacugacccggugaggcgggggggcgagcc
ccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauauugug
gcggccaagcguucauagcgacgucgcugaugucggcucuuccuaucauu
gugaagcagaauucaccaagcguuggauuguucacccacuaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacggcagcgccgcggagccucgguuggccucggauagccgg
ucccccgccgggguccggugcggagugcccuucguccugggaaacggggc
gcggccggagaggcggccgcccccucgcccgucacgcaccgcacguucgu
ggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggg
uuucguacguagcagagcagcucccucgcugcgaucuauugaaagucagc
ccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ie3 Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 T8 R11 R15 K28 S31 P33 R45 S46 R59 G60 H61 K63 K77 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 T8 R11 R15 K28 S31 P33 R45 S46 R59 G60 H61 K63 K77 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126

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:8ie3, PDBe:8ie3, PDBj:8ie3
• PDBsum: 8ie3
• PubMed: 37491604
• UniProt: P61254|RL26_HUMAN Large ribosomal subunit protein uL24 (Gene Name=RPL26)