Structure of PDB 8oj8 Chain LT Binding Site BS01

Receptor Information

>8oj8 Chain LT (length=159) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEFMA

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): T2 N3 T4 K5 G6 K7 R8 R9 G10 R12 Y13 M14 S16 R17 F19 H22 G23 K35 K36 K43 G46 Q49 K50 G51 H54 K55 H58 G59 K60 T61 T68 Q69 H70 K78 V80 K83 K87 R88 I89 R92 K97 K100 S101 R102 F105 R108 V109 K110 K116 K120 W125 V126 L128 K129 R130 F140 R142
• Binding residue (residue number reindexed from 1): T1 N2 T3 K4 G5 K6 R7 R8 G9 R11 Y12 M13 S15 R16 F18 H21 G22 K34 K35 K42 G45 Q48 K49 G50 H53 K54 H57 G58 K59 T60 T67 Q68 H69 K77 V79 K82 K86 R87 I88 R91 K96 K99 S100 R101 F104 R107 V108 K109 K115 K119 W124 V125 L127 K128 R129 F139 R141

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• 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: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)