Structure of PDB 8oj0 Chain LP Binding Site BS01

Receptor Information

>8oj0 Chain LP (length=153) Species: 9606 (Homo sapiens)

VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKE

Ligand information

>8oj0 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: 8oj0 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): V2 R3 Y4 L6 K16 R18 S20 R23 H25 K27 N28 R30 Q34 K43 R62 Y63 N64 G65 G66 G68 R69 A71 Q72 K74 Q75 W78 Q80 R82 W83 P84 K86 N97 S100 N101 H116 Q118 V119 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 P138 Y139 M140 S141
• Binding residue (residue number reindexed from 1): V1 R2 Y3 L5 K15 R17 S19 R22 H24 K26 N27 R29 Q33 K42 R61 Y62 N63 G64 G65 G67 R68 A70 Q71 K73 Q74 W77 Q79 R81 W82 P83 K85 N96 S99 N100 H115 Q117 V118 R126 T128 Y129 R130 A131 H132 G133 R134 I135 N136 P137 Y138 M139 S140

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:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8oj0, PDBe:8oj0, PDBj:8oj0
• PDBsum: 8oj0
• PubMed: 38383785
• UniProt: P18621|RL17_HUMAN Large ribosomal subunit protein uL22 (Gene Name=RPL17)