Structure of PDB 7f5s Chain Lf Binding Site BS01

Receptor Information

>7f5s Chain Lf (length=109) Species: 9606 (Homo sapiens)

SGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVY
KAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRI
RVMLYPSRI

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

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 G3 R4 W6 K8 K15 R16 L18 R19 N20 Q21 R22 E23 H24 K29 Y34 R36 R46 Y51 K52 K54 N55 N56 T57 V58 P60 T67 R68 V69 W71 K73 R76 H78 G79 N80 S81 R85 K87 R89 S90 N91 P93 A94 R100 R102
• Binding residue (residue number reindexed from 1): S1 G2 R3 W5 K7 K14 R15 L17 R18 N19 Q20 R21 E22 H23 K28 Y33 R35 R45 Y50 K51 K53 N54 N55 T56 V57 P59 T66 R67 V68 W70 K72 R75 H77 G78 N79 S80 R84 K86 R88 S89 N90 P92 A93 R99 R101

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

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:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7f5s, PDBe:7f5s, PDBj:7f5s
• PDBsum: 7f5s
• PubMed: 35674491
• UniProt: P18077|RL35A_HUMAN Large ribosomal subunit protein eL33 (Gene Name=RPL35A)