Structure of PDB 8qfd Chain d Binding Site BS01

Receptor Information

>8qfd Chain d (length=105) Species: 9606 (Homo sapiens)

NEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTR
LNKAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNL
QTVNV

Ligand information

>8qfd Chain 5 (length=3130)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccggcgcgggacauguggcgu
acggaagacccgggggcccaaguccuucugaucgaggccccguggacggu
gugaggccgguagcggcccccgggucuucccggagucggguugcuuggga
augcagcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcac
gagaccgauagucaacaaguaccguaagggaaaguugaaaagaacuuuga
agagagaguucaagagggcgugaaaccguuaagagguaaacggguggggu
ccgcgcccggcaacccggcggcgccgccgccgggcgcauuuccaccgccg
cgaccggcuccgggacggcugggaaggccggggaaggugaguguuacagc
cccggcagcagcacucgccgaaucccggggccgagggagcgccgcgcucu
ccccgggccgggccaccccucccacggcgcgaccgcucggggcggacugu
ccccagugcgcaccgggcgggucgcgccgucgggcccggggggccacgag
cgcacggggucggcggcucggcuacccacccgacccgucuugaaacacgg
accaaggagucuaacacgugcgcgagucgggggcuacgaaagccgccgug
gcgcaaugaaggugaaggugggaucccgaggccgccgagggcgcaccacc
ggcccgucucgccggggagguggagcacgagcgcacguguuaggacccga
aagauggugaacuaugccugggcagggcgaagccagagucugguggaggu
ccguagcgguccugacgugcaaaucggucguccgaccuggguauaggggc
gaaagacuaaucgaaccaucuaguagcugguucccuccgaaguuucccuc
aggauagcuggcgcucuccgcaguuuuauccgguaaagcgaaugauuaga
ggaaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcgu
ggagccgggcguggaaugcgagugccuagugggccacuuuugguaagcag
aacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccg
acgcucaucagaccccaaaaagguguugguugauucaacuagcccugaaa
auggauggcgcuggagcgucgggcccauacccggccgucgccggcagucg
gacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagcc
uagggcgcgggcccggguggagccgccgcaggugcagaucuuggugguag
uagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguucc
augugaacagcaguugaacaugggucagucgguccugagagaugggcgag
cgccguuccgaagggaucggcgaucgaaagggagucggguucagaucccc
gaauccggagcggagaugggcguccagugcgguaacgcgaccgaucccgg
agaagccggcgggagccccggggagaguucucuuuucuuugugaagggca
gggcgcccuggaauggguucgccccgagagaggggcccgugccuuggaaa
gcgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaaau
ccgggggagaggguguaaaucucgcgccgggccguacccauauccgcagc
aggucuccaaggugaacagccucuggcauguuggaacaauguagguaagg
gaagucggcaagccggauccguaacuucgggauaaggauuggcucuaagg
gccgacuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaa
caaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuucugc
ccagugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaac
ggcggcuuaagguagccaaaugccucgucaucuaauuagugacgcgcaug
aauggaugaacgagauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguu
gagcuugacucuagucuggcacggugaagagacaugagagguguagaaua
agugggaggcggccgccggugaaauaccacuacucugaucguuuuuucac
ugacccggugaggcggggguucuggcgccaagcgcccggccgggcgcgac
ccgcuccggggacagugccagguggggaguuugacuggggcgguacaccu
gucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaac
cucccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguac
gaauacagaccgugaaagcggggccucacgauccuucugaccuuuugggu
uuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugugg
cggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcuc
uuccuaucauugugaagcagaauucaccaagcguuggauuguucacccac
uaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuu
acccuacugaugauguguuguugccaugguaauccugcucaguacgagag
gaaccgcagguucagacauuugguguaugugcuuggcugaggagccaaug
gggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaa
ucccgcccaggcggaacgauaagcgccccucgguuggccucggauagccg
gccggugcggagugcccucguccugggaaacggggccggaaaggcggccg
ccgcccgucacgcaccgcacguucguggggaggcgcuaaaccauucguag
acgaccugcuugggucgggguuucguacguagcagagcagugcgaucuau
ugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qfd The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): R23 T26 H30 K31 R32 H34 G35 F38 K39 R41 R44 K47 R50 I64 T66 N69 K70 W73 K75 I77 R78 N79 Y82 R83 N116 L117 Q118
• Binding residue (residue number reindexed from 1): R6 T9 H13 K14 R15 H17 G18 F21 K22 R24 R27 K30 R33 I47 T49 N52 K53 W56 K58 I60 R61 N62 Y65 R66 N99 L100 Q101

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:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qfd, PDBe:8qfd, PDBj:8qfd
• PDBsum: 8qfd
• PubMed: 38383789
• UniProt: P62899|RL31_HUMAN Large ribosomal subunit protein eL31 (Gene Name=RPL31)