Structure of PDB 8fkr Chain SS Binding Site BS01

Receptor Information

>8fkr Chain SS (length=235) Species: 9606 (Homo sapiens)

GDEYAEDSSDEEDIRNTVGNVPLEWYDDFPHVGYDLDGRRIYKPPDYWRT
VQDPMTGRDLRLTDEQVALVRRLQSGQFGDVGFNPYEPAVDFFSGDVMIH
PVTNRPADKRSFIPSLVEKEKVSRMVHAIKMGWIQPRRPRDPTPSFYDLW
ARHKMHVPAPKLALPGHAESYNPPPEYLLSEEERLAWEQQEPGERKLSFL
PRKFPSLRAVPAYGRFIQERFERCLDLYLCPRQRK

Ligand information

>8fkr Chain L3 (length=1767)

gcgaccucagaucagacguggcgacccgcugagcauauuagucagcggag
gagaagaaacuaaccaggauucccucaguaacggcgagugaacagggaag
agcccagcgccgaauccccgccccgggggcgcgggacauguggcguacgg
aagacccgcuccccggcgccgcucguggggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaagua
ccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggcgu
gaaaccguuaagaggacgggugggguccgcgcaguccgcccggaggauuc
aacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcgccg
cgaccggcuccgggacggcugggaaggcccggcggggaagguggcucggg
cccgaguguuacagcccccccggcagcagcacucgccgaaucccggggcc
gagcggcgacgucggcuacccacccgacccgucuacacggaccaaggagu
cuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgcaag
gugggaucccgaggccaguccgccgagggcgcaccaccggcccgucucgc
ccggggagguggagcacgagcgcacguguuaggacccgaagcugguuccc
uccgaaguuucccucaggauagcuggcgcucucgcaguuuuauccggggu
aagaagcccggcucgagccgggcguggaaugcgagugccuagugggccac
uuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaag
gcgcccgaugccgacgcucacccagaaaagguguugguugauauagacag
caggacgguggccauggaagucggaauccgcuaaggaguguguaacaacu
caccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucggg
cccauacccggccgucgccggcagucgagaguggacggcgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaug
uuggaacaauguaggaccuacuauccagcgaaaccagccaagcuuggcuc
agccuggcuuguggcggccaagcgcgacgucgcuuuuugugugaagcaga
auucaccaaacugaugauguguuguugccaugguaauccugcucaguacg
agaggaaccgcagguucagacauuugguguaugugcuuggcugaggagcc
aauggggcgaagcuaccaucugugggauuaugacugaacgccucuaaguc
agaaucccgcccaggcggaacgauagcgccgcggagccucgguuggccuc
ggauagccgguccccgggguccggugcggagugcccuucguccugggaaa
cggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcac
guucguggggaaccuggcgcuaaaccauucguagacgaccugcugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaagag
cccucgacacgguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkr Principles of human pre-60 S biogenesis.
• Resolution: 2.89 Å
• Binding residue (original residue number in PDB): R239 D242 K243 R244 S245 S249 V251 K255 S257 H261 K264 M265 W267 R271
• Binding residue (residue number reindexed from 1): R105 D108 K109 R110 S111 S115 V117 K121 S123 H127 K130 M131 W133 R137

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000460 maturation of 5.8S rRNA
• 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
• GO:1901796 regulation of signal transduction by p53 class mediator

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:0070545 PeBoW complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkr, PDBe:8fkr, PDBj:8fkr
• PDBsum: 8fkr
• PubMed: 37410842
• UniProt: Q14137|BOP1_HUMAN Ribosome biogenesis protein BOP1 (Gene Name=BOP1)