Structure of PDB 8oj5 Chain LJ Binding Site BS01

Receptor Information

>8oj5 Chain LJ (length=175) Species: 9606 (Homo sapiens)

QDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSK
ARYTVRSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDT
GNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIG
AKHRISKEEAMRWFQQKYDGIILPG

Ligand information

>8oj5 Chain 5 (length=3474)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguca
acaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaag
agggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcc
cggaggauucaacccggcggcggguccggccgugccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccggggggccgggccaccccucccacggcgcg
accgcucggggcggacuguccccagugcgccccgggcgggucgcgccguc
gggcccggggggccacgcgcgcgucccccgggggacggcggagcgagcgc
acggggucggcggcgacgucggcuacccacccgacccgucuugaaacacg
gaccaaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgc
cguggcgcaaugaaggugaaggccggcgccggccgaggugggaucccgag
gccucuccaguccgccgagggcgcaccaccggcccgucucgcgggaggug
gagcacgagcgcacguguuaggacccgaaagauggugaacuaugccuggg
cagggcgaagccagaggaaacucugguggagguccguagcgguccugacg
ugcaaaucggucguccgaccuggguauaggggcgaaagacuaaucgaacc
aucuaguagcugguucccuccgaaguuucccucaggauagcuggcgcucu
cgcagacccgacgcaguuuuauccgguaaagcgaaugauuagaggucuug
gggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcc
cggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcca
cuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaa
ggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugaua
uagacagcgccgaaucaacuagcccugaaaauggauggcgcuggagcguc
gggcccauacccggccgucgccggcagucgagaguggacgggagccccgc
ggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagc
cuagggcgcgggcccggguggagccgccgcaggugcagaucuugguggua
guagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguuc
caugugaacagcaguugaacaugggucagucgguccugagagaugggcga
gcgccguuccgaagggacgggcgcccucggccgaucgaaagggagucggg
uucagauccccgaauccggagcggagaugggcgccgcgaggcguccagug
cgguaacgcgaccgaucccggagaagccggcgggagccccggggagaguu
cucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgaga
gaggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugag
cucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccg
ggccguacccauauccgcagcaggucuccaaggugaacagccucuggcau
guuggaacaauguagguaagggaagucggcaagccggauccguaacuucg
ggauaaggauuggcucuaagggcugguagcagccgacuuagaacuggugc
ggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggccc
gcggcggguguugacgcgaugugauuucugcccagugcucugaaugucaa
agugaagaaauucaaugaagcgcggguaaacggcgggaguacucucuuaa
gguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaagagacaugagagguguagaauaagugggaggc
ccgccggugaaauaccacuacucugauguuuuuucacugacccggugagg
cgggggggcgaucucgcuucuggcgccaagcgcccggccgcggccgggcg
cgacccgcuccggggacagugccagguggggaguuugacuggggcgguac
accugucaaacgguaacgcagguguccuaaggcgagcucagggaggacag
aaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuuuca
guacgaauacagaccgugaaagcggggccucacgauccuucugaccuuuu
ggguuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuu
guggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucg
gcucuuccuaucauugugaagcagaauucaccaagcguuggauuguucac
ccacuaauagggaacgugagcuggguuuagaccgucgugagacagguuag
uuuuacccuacugaugauguguuguugccaugguaauccugcucaguacg
agaggaaccgcagguucagacauuugguguaugugcuuggcugaggagcc
aauggggcgaagcuaccaucugugggauuaugacugaacgccucuaaguc
agaaucccgcccaggcggaacgauacggcagcgccgcggagccucgguug
gccucggauagccgguccccgggguccggugcggagugcccuucguccug
ggaaacggggcgcggcuggaaaggcggccgcccccucgcccgucacgcac
cgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugcuu
cugggucgggguuucguacguagcagagcagcgcugcgaucuauugaaag
ucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8oj5 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K19 C21 N23 C25 G27 S51 A53 R54 F60 H71 N97 N98 S100 T102 N104 G106 F107 G108 G127 D129 Y131 K145
• Binding residue (residue number reindexed from 1): K17 C19 N21 C23 G25 S49 A51 R52 F58 H69 N95 N96 S98 T100 N102 G104 F105 G106 G125 D127 Y129 K143

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006605 protein targeting
• GO:0010628 positive regulation of gene expression
• GO:0032092 positive regulation of protein binding
• GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
• GO:0034504 protein localization to nucleus
• GO:0042273 ribosomal large subunit biogenesis
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8oj5, PDBe:8oj5, PDBj:8oj5
• PDBsum: 8oj5
• PubMed: 38383785
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)