Structure of PDB 8ir3 Chain Y Binding Site BS02

Receptor Information

>8ir3 Chain Y (length=167) Species: 9606 (Homo sapiens)

VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKEQIVPKPEEEVAQKK

Ligand information

>8ir3 Chain 2 (length=3541)

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
gacgcccgccacgcaguuuuauccgguaaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggcccuc
ggccgaucgaaagggagucggguucagauccccgaauccggaguggcgga
gaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaa
gccggcgggagccccggggagaguucucuuuucuuugugaagggcagggc
gcccuggaauggguucgccccgagagaggggcccgugccuuggaaagcgu
cgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauccgg
gggagaggguguaaaucucgcgccgggccguacccauauccgcagcaggu
cuccaaggugaacagccucuggcauguuggaacaauguagguaagggaag
ucggcaagccggauccguaacuucgggauaaggauuggcucuaagggcug
ggucggucgcggccggcgccuagcagccgacuuagaacuggugcggacca
ggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcg
gguguugacgcgaugugauuucugcccagugcucugaaugucaaagugaa
gaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucuua
agguagccaaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaaguuuuuucacugacccgguga
ggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugggcgguacaccugucaaacgguaacgcaggugucaaggcgagcu
cagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuuga
ucuugauuuucaguacgaauacagaccgugaaagcggggccucacgaucc
uucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacagg
guggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuuc
gaugucggcucuuccuaucauugugaagcagaauucaccaagcguuggau
uguucacccacuaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugauguguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauacggcagcgccgcggagcc
ucgguuggccucggauagccggucccccgccgggguccggugcggagugc
ccuucguccugggaaacggggcgcggccggagaggcggccgcccccucgc
ccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucguag
acgaccugcuucugggucgggguuucguacguagcagagcagcucccucg
cugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ir3 Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): V2 R3 Y4 L6 K16 R18 S20 H25 R30 Q34 K37 K43 K55 R62 Y63 G65 G66 R69 A71 Q72 K74 Q75 W78 Q80 R82 W83 K86 S100 N101 V119 R127 Y130 R131 A132 N137 P138 Y139 M140 S141
• Binding residue (residue number reindexed from 1): V1 R2 Y3 L5 K15 R17 S19 H24 R29 Q33 K36 K42 K54 R61 Y62 G64 G65 R68 A70 Q71 K73 Q74 W77 Q79 R81 W82 K85 S99 N100 V118 R126 Y129 R130 A131 N136 P137 Y138 M139 S140

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ir3, PDBe:8ir3, PDBj:8ir3
• PDBsum: 8ir3
• PubMed: 37491604
• UniProt: P18621|RL17_HUMAN Large ribosomal subunit protein uL22 (Gene Name=RPL17)