Structure of PDB 8oj8 Chain LM Binding Site BS01

Receptor Information

>8oj8 Chain LM (length=136) Species: 9606 (Homo sapiens)

VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMP
FKCMQLTDFILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERK
AKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALLK

Ligand information

>8oj8 Chain 5 (length=3515)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguca
acaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaag
agggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcc
cggaggauucaacccggcggcggguccggccgugucggcgcggcggaucu
uucccggcgggggaccgucccccgaccggcgaccggccgccgccgggcgc
auuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaagg
cccggcggggaagguggcucgggggcccccgaguguuacagcccccccgg
cagcagcacucgccgaaucccggggccgagggagcgagacccgucgccgc
gcucuccccccggggggccgggccaccccucccacggcgcgaccgcucgg
ggcggacuguccccagugcgccccgggcgggucgcgccgucgggcccggg
gggccacgcgcgcgucccccgggggacggcggagcgagcgcacggggucg
gcggcgacgucggcuacccacccgacccgucuugaaacacggaccaagga
gucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgca
augaaggugaaggccggcgccggccgaggugggaucccgaggccucucca
guccgccgagggcgcaccaccggcccgucucgcgggagguggagcacgag
cgcacguguuaggacccgaaagauggugaacuaugccugggcagggcgaa
gccagaggaaacucugguggagguccguagcgguccugacgugcaaaucg
gucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguag
cugguucccuccgaaguuucccucaggauagcuggcgcucucgcagaccc
gacgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccgaaa
cgaucucaaccuauucucaaacuuuaaauggguaagaagcccggcucgcu
ggcguggagccgggcguggaaugcgagugccuagugggccacuuuuggua
agcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccga
ugccgacgcucaucagaccccagaaaagguguugguugauauagacagcg
ccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccaua
cccggccgucgccggcagucgagaguggacgggagccccgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaau
auucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaac
agcaguugaacaugggucagucgguccugagagaugggcgagcgccguuc
cgaagggacgggcgcccucggccgaucgaaagggagucggguucagaucc
ccgaauccggagcggagaugggcgccgcgaggcguccagugcgguaacgc
gaccgaucccggagaagccggcgggagccccggggagaguucucuuuucu
uugugaagggcagggcgcccuggaauggguucgccccgagagaggggccc
gugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcug
gcccuugaaaauccgggggagaggguguaaaucucgcgccgggccguacc
cauauccgcagcaggucuccaaggugaacagccucuggcauguuggaaca
auguagguaagggaagucggcaagccggauccguaacuucgggauaagga
uuggcucuaagggcugguagcagccgacuuagaacuggugcggaccaggg
gaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggu
guugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaugaagcgcggguaaacggcgggaguacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggaugaacgagauucc
cacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuu
ggcggaaucagcggggaaagaagacccuguugagcuugacucuagucugg
cacggugaagagacaugagagguguagaauaagugggaggcccgccggug
aaauaccacuacucugauguuuuuucacugacccggugaggcgggggggc
gaucucgcuucuggcgccaagcgcccggccgcggccgggcgcgacccgcu
ccggggacagugccagguggggaguuugacuggggcgguacaccugucaa
acgguaacgcagguguccuaaggcgagcucagggaggacagaaaccuccc
guggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaaua
cagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaa
gcaggaggugucagaaaaguuaccacagggauaacuggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugauguguuguugccaugguaauccugcucaguacgagaggaacc
gcagguucagacauuugguguaugugcuuggcugaggagccaauggggcg
aagcuaccaucugugggauuaugacugaacgccucuaagucagaaucccg
cccaggcggaacgauacggcagcgccgcggagccucgguuggccucggau
agccgguccccgggguccggugcggagugcccuucguccugggaaacggg
gcgcggcuggaaaggcggccgcccccucgcccgucacgcaccgcacguuc
guggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgg
gguuucguacguagcagagcagcgcugcgaucuauugaaagucagcccuc
gacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8oj8 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): F3 R5 F17 P19 H20 D29 N34 Q44 V45 R46 K53 Q56 P65 H69 Q70 K71 Y72 R74 W91 K94 R98 K101 M113 K114 K116 K117 M118 N120 R121 K132
• Binding residue (residue number reindexed from 1): F2 R4 F16 P18 H19 D28 N33 Q43 V44 R45 K52 Q55 P64 H68 Q69 K70 Y71 R73 W90 K93 R97 K100 M112 K113 K115 K116 M117 N119 R120 K131

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8oj8, PDBe:8oj8, PDBj:8oj8
• PDBsum: 8oj8
• PubMed: 38383785
• UniProt: P50914|RL14_HUMAN Large ribosomal subunit protein eL14 (Gene Name=RPL14)