Structure of PDB 8ir3 Chain T Binding Site BS01

Receptor Information

>8ir3 Chain T (length=266) Species: 9606 (Homo sapiens)

TKRAKRFLEKREPKLNENIKNAMLIKGGNANATVTKVLKDVYALKKPYGV
LYKKKNITRPFEDQTSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGRMYDY
HVLDMIELGIENFVSLKDIKNSKCPEGTKPMLIFAGDDFDVTEDYRRLKS
LLIDFFRGPTVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKSGRTPRI
ELEEMGPSLDLVLRRTHLASDDLYKLSMKMPKNISHDTFGTTYGRIHMQK
QDLSKLQTRKMKGLKK

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

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

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): R14 A15 R17 F18 N27 Y63 K65 F80 K84 N253 H267 M268 K270 K282
• Binding residue (residue number reindexed from 1): R3 A4 R6 F7 N16 Y52 K54 F69 K73 N233 H247 M248 K250 K262

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1902570 protein localization to nucleolus

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome
• GO:0005730 nucleolus

External links

• PDB: RCSB:8ir3, PDBe:8ir3, PDBj:8ir3
• PDBsum: 8ir3
• PubMed: 37491604
• UniProt: Q9H7B2|RPF2_HUMAN Ribosome production factor 2 homolog (Gene Name=RPF2)