Structure of PDB 8ink Chain e Binding Site BS01

Receptor Information

>8ink Chain e (length=131) Species: 9606 (Homo sapiens)

SGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGD
MVMATVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNK
GEMKGSAITGPVAKECADLWPRIASNAGSIA

Ligand information

>8ink Chain 2 (length=3495)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaacacggaccaaggagucuaacacgugcgcga
gucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgg
cgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgagg
gcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacgag
cgcacguguuaggacccgaaagauggugaacuaugccugggcagggcgaa
gccagaggaaacucugguggagguccguagcgguccugacgugcaaaucg
gucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguag
cugguucccuccgaaguuucccucaggauagcuggcgcucucgcagaccc
gacgcccgccacgcaguuuuauccgguauggguaagaagcccggcucgcu
ggcguggagccgggcguggaaugcgagugccuagugggccacuuuuggua
agcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccga
ugccgacgcucaucagacccagaaaagguguugguugauauagacagcag
gacgguggccauggaagucggaauccgcuaaggaguguguaacaacucac
cugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggccc
auacccggccgucgccggcagucgagaguggacgggagcggcggcccgga
gccccgcggacgcuacgccgcgacgaguaggagggccgcugcggugagcc
uugaagccuagggcgcgggcccggguggagccgccgcaggugcagaucuu
ggugguaguagcaaauauucaaacgagaacuuugaaggccgaaguggaga
aggguuccaugugaacagcaguugaacaugggucagucgguccugagaga
ugggcgagcgccguuccgaagggacgggcgauggccuccguugcccucgg
ccgaucgaaagggagucggguucagauccccgaauccggaguggcggaga
ugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaagc
cggcgggagccccggggagaguucucuuuucuuugugaagggcagggcgc
ccuggaauggguucgccccgagagaggggcccgugccuuggaaagcgucg
cgguuccggcggcguccggugagcucucgcuggcccuugaaaauccgggg
gagaggguguaaaucucgcgccgggccguacccauauccgcagcaggucu
ccaaggugaacagccucuggcauguuggaacaauguagguaagggaaguc
ggcaagccggauccguaacuucgggauaaggauuggcucuaagggcuggg
ucggucgcggccggcgccuagcagccgacuuagaacuggugcggaccagg
ggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggg
uguugacgcgaugugauuucugcccagugcucugaaugucaaagugaaga
aauucaaugaagcgcggguaaacggcgggaguacucucuuaagaacgaga
uucccacugucccuaccuacuauccagcgaaaccacagccaagggaacgg
gcuuggcggaaucagcggggaaagaagacccuguugagcuugacucuagu
cuggcacggugaaguuuuuucacugacccggugaggcgggggggcgagcc
ccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuuccugucgcagg
uguccuaaggcgagcucagggaggacagaaaccucccguggagcagaagg
gcaaaagcucgcuugaucuugauuuuuacgaauacagaccgugaaagcgg
ggccgauccuucugaccuuuuggguuuuaagcaggagguaaguuaccaca
gggauaggcuuguggcggccaagcguucauagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauacggcagcgccgcgg
agccucgguuggccucggauagccggucccccgccgggguccggugcgga
gugcccuucguccugggaaacggggcgcggccggagaggcggccgccccc
ucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauuc
guagacgaccugcuucugggucgggguuucguacguagcagagcagcucc
cucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ink Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): F14 R15 S17 G19 P21 G23 S41 K43 G44 K46 R48 L49 N50 R51 L52 R85 K86 R89 F95
• Binding residue (residue number reindexed from 1): F5 R6 S8 G10 P12 G14 S32 K34 G35 K37 R39 L40 N41 R42 L43 R76 K77 R80 F86

Gene Ontology

Molecular Function

• GO:0001223 transcription coactivator binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0070180 large ribosomal subunit rRNA binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006610 ribosomal protein import into nucleus
• GO:0008284 positive regulation of cell population proliferation
• GO:0010628 positive regulation of gene expression
• GO:0032986 protein-DNA complex disassembly
• GO:0050821 protein stabilization
• GO:0070314 G1 to G0 transition
• GO:0072717 cellular response to actinomycin D
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1903450 regulation of G1 to G0 transition
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ink, PDBe:8ink, PDBj:8ink
• PDBsum: 8ink
• PubMed: 37491604
• UniProt: P62829|RL23_HUMAN Large ribosomal subunit protein uL14 (Gene Name=RPL23)