Structure of PDB 8qfd Chain R Binding Site BS01

Receptor Information

>8qfd Chain R (length=149) Species: 9606 (Homo sapiens)

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLII
RKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRI
LRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLKADKA

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 K8 R9 G18 K19 K20 K21 W23 L24 P26 S37 R38 Q39 Q40 R42 K43 T56 H58 S59 R60 R62 R64 R70 R74 H75 M76 G77 I78 G79 K80 R81 K82 G83 T84 N86 R88 M89 P90 K92 W95 M96 R97 R100 R103 R104 R108 R110 R117 H118 Y120 H121 Y124 L125 K128 G129 N130 K135 R136
• Binding residue (residue number reindexed from 1): R4 K7 R8 G17 K18 K19 K20 W22 L23 P25 S36 R37 Q38 Q39 R41 K42 T55 H57 S58 R59 R61 R63 R69 R73 H74 M75 G76 I77 G78 K79 R80 K81 G82 T83 N85 R87 M88 P89 K91 W94 M95 R96 R99 R102 R103 R107 R109 R116 H117 Y119 H120 Y123 L124 K127 G128 N129 K134 R135

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:0005730 nucleolus
• 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:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8qfd, PDBe:8qfd, PDBj:8qfd
• PDBsum: 8qfd
• PubMed: 38383789
• UniProt: P84098|RL19_HUMAN Large ribosomal subunit protein eL19 (Gene Name=RPL19)