Structure of PDB 7f5s Chain LX Binding Site BS01

Receptor Information

>7f5s Chain LX (length=119) Species: 9606 (Homo sapiens)

KKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAM
KKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAY
VRLAPDYDALDVANKIGII

Ligand information

>7f5s Chain L5 (length=3715)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcggccggggggggccgggcc
accccucccacggcgcgaccgcucggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccga
agagggggacggcggagcgagcgcacggggucggcggcgacgucggcuac
ccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcga
gucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgg
cgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgagg
gcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacgag
cgcacguguuaggacccgaaagauggugaacuaugccugggcagggcgaa
gccagaggaaacucugguggagguccguagcgguccugacgugcaaaucg
gucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguag
cugguucccuccgaaguuucccucaggauagcuggcgcucucgcagaccc
gacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuug
gggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcc
cggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcca
cuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaa
ggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugaua
uagacagcaggacgguggccauggaagucggaauccgcuaaggagugugu
aacaacucaccugccgaaucaacuagcccugaaaauggauggcgcuggag
cgucgggcccauacccggccgucgccggcagucgagaguggacgggagcg
gcggagccccgcggacgcuacgccgcgacgaguaggagggccgcugcggu
gagccuugaagccuagggcgcgggcccggguggagccgccgcaggugcag
aucuuggugguaguagcaaauauucaaacgagaacuuugaaggccgaagu
ggagaaggguuccaugugaacagcaguugaacaugggucagucgguccug
agagaugggcgagcgccguuccgaagggacgggcgauggccuccguugcc
cucggccgaucgaaagggagucggguucagauccccgaauccggaguggc
ggagaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccgga
gaagccggcgggagccccggggagaguucucuuuucuuugugaagggcag
ggcgcccuggaauggguucgccccgagagaggggcccgugccuuggaaag
cgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaaauc
cgggggagaggguguaaaucucgcgccgggccguacccauauccgcagca
ggucuccaaggugaacagccucuggcauguuggaacaauguagguaaggg
aagucggcaagccggauccguaacuucgggauaaggauuggcucuaaggg
cugggucggucgggccggcgccuagcagccgacuuagaacuggugcggac
caggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcgg
cggguguugacgcgaugugauuucugcccagugcucugaaugucaaagug
aagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucu
uaagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggau
gaacgagauucccacugucccuaccuacuauccagcgaaaccacagccaa
gggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuug
acucuagucuggcacggugaagagacaugagagguguagaauaaguggga
ggcccccugcgggccgccggugaaauaccacuacucugaucguuuuuuca
cugacccggugaggcgggggggcgagccccgaggggcucucgcuucuggc
gccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacag
ugccagguggggaguuugacuggggcgguacaccugucaaacgguaacgc
agguguccuaaggcgagcucagggaggacagaaaccucccguggagcaga
agggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccguga
aagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucau
agcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauuguga
agcagaauucaccaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaug
uguuguugccaugguaauccugcucaguacgagaggaaccgcagguucag
acauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccau
cugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgga
acgauacggcagcgccgcggagccucgguuggccucggauagccgguccc
ccgccgggguccggugcggagugcccuucguccugggaaacggggcgcgg
ccggagaggcggccgcccccucgcccgucacgcaccgcacguucgugggg
aaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuuc
guacguagcagagcagcucccucgcugcgaucuauugaaagucagcccuc
gacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7f5s METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance.
• Resolution: 2.72 Å
• Binding residue (original residue number in PDB): K39 P44 T45 R47 R48 K50 T51 R53 L54 R56 Q57 P58 K59 Y60 R62 T83 S85 K89 N93 N105 K106 H107 K123 N125 T126 L127 I128 P130 K134 K135 Y137 R139
• Binding residue (residue number reindexed from 1): K2 P7 T8 R10 R11 K13 T14 R16 L17 R19 Q20 P21 K22 Y23 R25 T46 S48 K52 N56 N68 K69 H70 K86 N88 T89 L90 I91 P93 K97 K98 Y100 R102

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0045296 cadherin binding
• GO:1904841 TORC2 complex binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7f5s, PDBe:7f5s, PDBj:7f5s
• PDBsum: 7f5s
• PubMed: 35674491
• UniProt: P62750|RL23A_HUMAN Large ribosomal subunit protein uL23 (Gene Name=RPL23A)