Structure of PDB 8qfd Chain I Binding Site BS01

Receptor Information

>8qfd Chain I (length=201) Species: 9606 (Homo sapiens)

GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGH
MVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINK
GMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQ
KIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPSRGPLDKWRALH
S

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): R3 R4 A6 R7 K13 N14 K15 P16 F22 R24 D35 K39 E63 K74 R90 H92 F94 R98 G114 M115 R116 G117 A118 F119 G120 Q133 F157 K158 P160 D193 G194 C195 K198
• Binding residue (residue number reindexed from 1): R2 R3 A5 R6 K12 N13 K14 P15 F21 R23 D34 K38 E62 K73 R89 H91 F93 R97 G101 M102 R103 G104 A105 F106 G107 Q120 F144 K145 P147 D180 G181 C182 K185

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045182 translation regulator activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0043066 negative regulation of apoptotic process
• GO:1990403 embryonic brain development

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005790 smooth endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qfd, PDBe:8qfd, PDBj:8qfd
• PDBsum: 8qfd
• PubMed: 38383789
• UniProt: P27635|RL10_HUMAN Large ribosomal subunit protein uL16 (Gene Name=RPL10)