Structure of PDB 8oj8 Chain LL Binding Site BS01

Receptor Information

>8oj8 Chain LL (length=201) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
A

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): A2 S4 R5 M8 L10 K11 H13 F14 H15 K16 W18 Q19 W25 Q28 P29 R31 K32 I33 R35 R36 K37 R39 Q40 K42 R56 V59 R60 P62 R65 Y66 H67 R71 G73 R74 L78 K88 R92 D99 P100 R101 R102 R103 S106 R129 R158 N159 K163 K165 R183 R186 I194 K197
• Binding residue (residue number reindexed from 1): A1 S3 R4 M7 L9 K10 H12 F13 H14 K15 W17 Q18 W24 Q27 P28 R30 K31 I32 R34 R35 K36 R38 Q39 K41 R55 V58 R59 P61 R64 Y65 H66 R70 G72 R73 L77 K87 R91 D98 P99 R100 R101 R102 S105 R128 R157 N158 K162 K164 R182 R185 I193 K196

Gene Ontology

Molecular Function

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

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8oj8, PDBe:8oj8, PDBj:8oj8
• PDBsum: 8oj8
• PubMed: 38383785
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)