Structure of PDB 8oj8 Chain LN Binding Site BS01

Receptor Information

>8oj8 Chain LN (length=203) Species: 9606 (Homo sapiens)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

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): G2 Y4 Q8 R12 K14 Q15 R24 W28 R31 H37 P40 R41 R44 K47 R49 R50 L51 A55 R65 R67 R68 G69 G70 R71 K72 R73 P74 K77 Y81 G82 K83 P84 V85 H86 H87 N90 Q91 K93 F94 A95 R96 S97 E104 R105 R108 A112 S125 Y127 F138 R144 W150 H156 K157 H158 M161 R162 L164 S166 S171 R172 K176 G177 H178 K179 H181 H182 G185 G186 S187 R189 W192 R193 R194 R195 H201 R202 Y203 R204
• Binding residue (residue number reindexed from 1): G1 Y3 Q7 R11 K13 Q14 R23 W27 R30 H36 P39 R40 R43 K46 R48 R49 L50 A54 R64 R66 R67 G68 G69 R70 K71 R72 P73 K76 Y80 G81 K82 P83 V84 H85 H86 N89 Q90 K92 F93 A94 R95 S96 E103 R104 R107 A111 S124 Y126 F137 R143 W149 H155 K156 H157 M160 R161 L163 S165 S170 R171 K175 G176 H177 K178 H180 H181 G184 G185 S186 R188 W191 R192 R193 R194 H200 R201 Y202 R203

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:0006412 translation
• GO:0045471 response to ethanol

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0031672 A band
• GO:0044391 ribosomal subunit
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8oj8, PDBe:8oj8, PDBj:8oj8
• PDBsum: 8oj8
• PubMed: 38383785
• UniProt: P61313|RL15_HUMAN Large ribosomal subunit protein eL15 (Gene Name=RPL15)