Structure of PDB 8ir3 Chain u Binding Site BS02

Receptor Information

>8ir3 Chain u (length=75) Species: 9606 (Homo sapiens)

MKRPKLKKASKRMTCHKRYKIQKKVREHHRKLRKEAKKRGHKKPRKDPGV
PNSAPFKEALLREAELRKQRLEELK

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): M1 K2 R3 L6 K7 K8 S10 K11 R12 M13 T14 C15 H16 K17 Y19 K20 I21 K24 V25 R26 H28 R30 R33 R45 A54
• Binding residue (residue number reindexed from 1): M1 K2 R3 L6 K7 K8 S10 K11 R12 M13 T14 C15 H16 K17 Y19 K20 I21 K24 V25 R26 H28 R30 R33 R45 A54

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0017145 stem cell division
• GO:0019827 stem cell population maintenance
• GO:0032206 positive regulation of telomere maintenance
• GO:0033235 positive regulation of protein sumoylation
• GO:0042127 regulation of cell population proliferation
• GO:1902895 positive regulation of miRNA transcription
• GO:1904816 positive regulation of protein localization to chromosome, telomeric region

Cellular Component

• GO:0005615 extracellular space
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome
• GO:0005730 nucleolus
• GO:0016020 membrane
• GO:0016604 nuclear body
• GO:0030496 midbody

External links

• PDB: RCSB:8ir3, PDBe:8ir3, PDBj:8ir3
• PDBsum: 8ir3
• PubMed: 37491604
• UniProt: Q9BVP2|GNL3_HUMAN Guanine nucleotide-binding protein-like 3 (Gene Name=GNL3)