Structure of PDB 8fl4 Chain SM Binding Site BS01

Receptor Information

>8fl4 Chain SM (length=399) Species: 9606 (Homo sapiens)

GGLEKKKYERGSATNYITRNKARKKLQLSLADFRRLCILKGIYPHEPKHK
KKVNKGSTAARTFYLIKDIRFLLHEPIVNKFREYKVFVRKLRKAYGKSEW
NTVERLKDNKPNYKLDHIIKERYPTFIDALRDLDDALSMCFLFSTFPRTG
KCHVQTIQLCRRLTVEFMHYIIAARALRKVFLSIKGIYYQAEVLGQPIVW
ITPYAFSHDHPTDVDYRVMATFTEFYTTLLGFVNFRLYQLLNLHYPPKLE
GQGTYALDSESCMEKLAALSASLARVVVSAQEEDRRKELEAQEKHKKLFE
GLKFFLNREVPREALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIV
DRPGQQTSVIGRCYVQPQWVFDSVNARLLLPVAEYFSGVQLPPHLSPFV

Ligand information

>8fl4 Chain L3 (length=3486)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucuugaaacacggaccaaggagucuaacacgug
cgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaag
gccgcggccgaggugggaucccgaggcccgccgagggcgcaccaccggcc
cgucucgcccgccgcgccggggagguggagcacgagcgcacguguuagga
cccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacuc
ugguggagguccguagcgguccugacgugcaaaucggucguccgaccugg
guauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccga
aguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcg
aaugauuagaggucuuggggccggaucucaaccuauucucggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagugacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgaugcccucgaucgaaagggagucggguucagauccccgaauccg
gaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccga
ucccggagaagccggcgggagccccggggagaguucucuuuucuuuguga
agggcagggcgcccuggaauggguucgccccgagagaggggcccgugccu
uggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuu
gaaaauccgggggagaggguguaaaucucgcgccgggccguacccauauc
cgcagcaggucuccaaggugaacagccucuggcauguuggaacaauguag
guaagggaagucggcaagccggauccguaacuucgggauaaggauuggcu
cuaagggcugggucggucgggcuggggcgcgaagcggggucccguggauc
gccccagccggccggcgccuagcagccgacuuagaacuggugcggaccag
gggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccggggugu
ugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaaau
ucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaaggua
gccaaaugccucgucaugugacgcgcaugaauggaugaacgagauuccca
cugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuugg
cggaaucagcggggaaagaagacccuguugagcuugacucuagucuggca
cggugaagagacaugagagguguagaauaagugggaggcggccgccggug
aaauaccacuacucugaucguuuuuucacugacccggugaggcggggggc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugguacaccugucaaacgguaacgcag
guguccuaaggcgagcucagggaggacagaaaccucccguggagcagaag
ggcaaaagcucgcuugaucuugauuuuguacgaauacagaccgugaaagc
ggggccucacccuucugaccuuuuggguuuuaagcaggaggaaguuacca
cagggauaacuggcuuguggcggccaagcgagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauagcgccgcggagccu
cgguuggccucggauagccgguccccgggguccggugcggagugcccuuc
guccugggaaacggggcgcggccggagaggcggccgcccccucgcccguc
acgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgac
cugcuucugggucgggguuucguacguagcagagcagcucccucgcugcg
aucuauugaaagucagcccucgacacaaggguuugu

........................<<<<<<.....<<....>>......>
>>>>.>.........<<....>>..<<<<<<.....<<.....>>....>
>>>>>..<<<...<<<<...<<<<<<<<<..>>>>>.>>>>.....>>>>
...<<<<<<<<<<...<<<<<<<<.<<<<<<<<<<....<<<<......>
>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>>>
>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....<<
<<<..((((((>>>>>..>>>.............................
.....<<....>>...............<<<......>>>..........
........................<<<<<<<<..<<<.<<...<<<<<<<
<.<<<.....<<<<<<<<<<<<<<<<<<.<<<<<.<<...<<<<<.<<..
.>>>>>>>>>>>>>>>>>>...>>>>>>>>>>>>>>......>>>.>>>.
>>>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<.
.....<<<<<<..>>>>>>.......>>>>>>.>>>........>>>>>>
..>>>>>>>>>>>...........<<<<<<.<<<<<..>>>>>.<<<<<<
.<<<<.<<<<<<<<<..>>>>>>.>>>...>>>>>>>>.>>..<<<<<<<
<<.......>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>
>...>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<
<<<..<<<...<<<<........>>>>.....>>>...<<....>>...<
<<<..>>>>..<<<<<...<<<..<<<..>>>..>>>....>>>>>.<<<
<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..
<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>
>>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>
>>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<<..
....<<<....>>>..<<<<<<<<<<...<<<.<<<<<<<<.........
...<<....<<<..<<<<<<.<.>.>>>>>>>>>..>>..>>>>>>...<
<<<<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>.>>>..<<
<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<.
..<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<
<.......<<<<<.<<<...<<.........>>...>>>.........<<
......>>...>>>>>...>>>>>>>>>>>>>..........))).>>..
.>>>>>..>>>...>>>>>>><<<<<<.<<<...........>>>>>>>>
>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>>>>>
>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<<<<<.
......>>>>>>.<<<.....<<<<<.<<...<<<<<....<<.....>>
..>>>>>....((<<<<<<...<<....<<<....>>>............
.<<<<...>>>>....>>....>>>..<<<<<........>>>>>))<<<
<.....<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..
<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....
<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>
>.....<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>....
.....>>>>>>>..>..........>>.>>..>>>>.>>>..>>.....<
<......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<
<<<.<<...............<<<<<....<<..>>.....>>>>><<.<
<<<<<<<<<<.<<<<<<<<.<<<<<<<<<....<<<<<..>>>>>....>
>>>>>>>>>>>>>>>>......>>>>>..>>>>>>.>>............
<<<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.>>>>..
....>>>>>>>.......<<<..<<<<<<....<<<.....<<<<....>
>>>.....>>>.>>>>..>>>>><<<<<<.......>>>>>>........
.....<<<<..<<<<<<>>>>>>.>>>>...........>>.>>>>>>>.
....>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>
....<<<<<..<<<........<<<<<.<<<<<<..<<<<<.<<<<<<<<
<.<<<<<<<<<<<<.<<<<..........<<<<<..<<<.>>>.......
.....>>>>>.>>>>.>>.>>>>>>>>>>...<<<<<.....<<<<....
............<<<<<<<<<<.......>>>>>>>>>>..>>>>..>>>
>>....>>>>>>>>>..>>>>>..<<.<<<<<<<.............>>>
>>>>>>...<<<<<<<...<<<<<<.......>>>>>>.....<<...((
(>>....>>>>>>>...<<<..<<<<.[[..>>>>..>>>.<<<....>>
>...))).]]<<<<<<<..<<<..)))))).>>>>>>>>>>.>>>>..>>
>>>>>.............<<<<<<...<<..>>...>>>>>>........
.........<<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<
<<.........>>>.....>>>>>..>...>>>>......<<<<<<<...
.>>>.>>>>........>>>.>>>>>.....<<<<<<.<..<<<..<.<<
<<<.................>>>>>.><<<<....<<<<....<<.<<<<
<<<]]].>>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<....
.......>>>>>...>>>>>.>>>...>.>>>>>>.<<<<<<.<<..<<<
<....<<<........<<<<<.<<<<>>>>.>>>>>.......>>>...<
<<..<<<<....<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..
>>>..............>>>>..>>>>>>>>.<<<<<.<...........
..>....<<.<<<<<<<.<<.....<<<<....<<<<<......>>>>>.
..>>>>....>>....>>>.>>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl4 Principles of human pre-60 S biogenesis.
• Resolution: 2.89 Å
• Binding residue (original residue number in PDB): G2 G3 K6 K7 K8 G12 S13 D214 V215 D216
• Binding residue (residue number reindexed from 1): G1 G2 K5 K6 K7 G11 S12 D213 V214 D215

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0043021 ribonucleoprotein complex binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0008283 cell population proliferation
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:0051726 regulation of cell cycle

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome
• GO:0005730 nucleolus
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0030687 preribosome, large subunit precursor
• GO:0070545 PeBoW complex

External links

• PDB: RCSB:8fl4, PDBe:8fl4, PDBj:8fl4
• PDBsum: 8fl4
• PubMed: 37410842
• UniProt: O00541|PESC_HUMAN Pescadillo homolog (Gene Name=PES1)