Structure of PDB 8qfd Chain T Binding Site BS01

Receptor Information

>8qfd Chain T (length=158) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEFM

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): T2 N3 T4 K5 G6 K7 R8 R9 R12 Y13 S16 F19 H22 G23 K35 D41 K43 G46 T47 Q49 G51 H54 K55 Y57 H58 G59 K60 T61 T68 Q69 H70 K78 V80 K83 L85 K87 R88 R92 K100 S101 R102 F105 R108 V109 K110 N112 W125 V126 K129 R130 F140 R142
• Binding residue (residue number reindexed from 1): T1 N2 T3 K4 G5 K6 R7 R8 R11 Y12 S15 F18 H21 G22 K34 D40 K42 G45 T46 Q48 G50 H53 K54 Y56 H57 G58 K59 T60 T67 Q68 H69 K77 V79 K82 L84 K86 R87 R91 K99 S100 R101 F104 R107 V108 K109 N111 W124 V125 K128 R129 F139 R141

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:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• 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: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)