Structure of PDB 8qfd Chain e Binding Site BS01

Receptor Information

>8qfd Chain e (length=128) Species: 9606 (Homo sapiens)

AALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKG
QILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAH
NVSSKNRKAIVERAAQLAIRVTNPNARL

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): R5 K14 K15 R16 T17 K18 K19 F20 R22 H23 Q24 D26 R27 Y28 K30 I31 N34 W35 R36 K37 R39 G40 I41 D42 N43 R44 R46 R47 R48 F49 K50 G51 Q52 N57 I58 G59 Y60 G61 S62 N63 K64 K65 K67 H68 K76 K83 E98 A100 H101 N102 S104 N107 R108 N124 R128
• Binding residue (residue number reindexed from 1): R4 K13 K14 R15 T16 K17 K18 F19 R21 H22 Q23 D25 R26 Y27 K29 I30 N33 W34 R35 K36 R38 G39 I40 D41 N42 R43 R45 R46 R47 F48 K49 G50 Q51 N56 I57 G58 Y59 G60 S61 N62 K63 K64 K66 H67 K75 K82 E97 A99 H100 N101 S103 N106 R107 N123 R127

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qfd, PDBe:8qfd, PDBj:8qfd
• PDBsum: 8qfd
• PubMed: 38383789
• UniProt: P62910|RL32_HUMAN Large ribosomal subunit protein eL32 (Gene Name=RPL32)