Structure of PDB 7f5s Chain Ll Binding Site BS01

Receptor Information

>7f5s Chain Ll (length=50) Species: 9606 (Homo sapiens)

SSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL

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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<......>>>>>...>.>.<<<.........>>>.....>>>>>......
>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>....
.<<<<<<.<..<<<....<<<<<.................>>>>>..<<<
<....<<<<....<<.<<<<<<<]]].>>>>>..>>.>>...>>>>...>
>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>...>.>
>>>>>.....<<<<<<<.<<..<<<<....<<<........<<<<<.<<<
<....>>>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<<
<<<......>>>>>>>>>>>...>>>>..>>>..............>>>>
..>>>>>>>>><<<<<....................<<.<<<<<<<.<<.
....<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.
>>>.>>..>>>>>..

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): S2 S3 H4 K5 K10 L13 Q17 I35 R36 Y37 N38 S39 R41 R42 H43 W44 R45 K48 L49 L51
• Binding residue (residue number reindexed from 1): S1 S2 H3 K4 K9 L12 Q16 I34 R35 Y36 N37 S38 R40 R41 H42 W43 R44 K47 L48 L50

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0002227 innate immune response in mucosa
• GO:0006412 translation
• GO:0019731 antibacterial humoral response
• GO:0050830 defense response to Gram-positive bacterium
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7f5s, PDBe:7f5s, PDBj:7f5s
• PDBsum: 7f5s
• PubMed: 35674491
• UniProt: P62891|RL39_HUMAN Large ribosomal subunit protein eL39 (Gene Name=RPL39)