Structure of PDB 8ir1 Chain S Binding Site BS01

Receptor Information

>8ir1 Chain S (length=135) Species: 9606 (Homo sapiens)

VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMP
FKCMQLTDFILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERK
AKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALL

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

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

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): F3 R5 F17 H20 D29 N34 Q44 R46 K53 Q56 P65 H66 H69 Q70 K71 Y72 R90 W91 K94 R98 M113 K114 K116 K117 M118 N120 R121 K132
• Binding residue (residue number reindexed from 1): F2 R4 F16 H19 D28 N33 Q43 R45 K52 Q55 P64 H65 H68 Q69 K70 Y71 R89 W90 K93 R97 M112 K113 K115 K116 M117 N119 R120 K131

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0014069 postsynaptic density
• 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:8ir1, PDBe:8ir1, PDBj:8ir1
• PDBsum: 8ir1
• PubMed: 37491604
• UniProt: P50914|RL14_HUMAN Large ribosomal subunit protein eL14 (Gene Name=RPL14)