Structure of PDB 8g61 Chain Ll Binding Site BS02

Receptor Information

>8g61 Chain Ll (length=50) Species: 9606 (Homo sapiens)

SSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL

Ligand information

>8g61 Chain L5 (length=3657)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccgcgggggaccgucccccgaccggcgaccggccgccg
ccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggc
ugggaaggcccggcggggaagguggcucgggggccccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccugggggggccgggccaccccucccacggcgcg
accgcucggggcggacuguccccagugcgccccgggcgggucgcgccguc
gggcccggggggccacgcgcgcgucccccgaagagggggacggcggagcg
agcgcacggggucggcggcgacgucggcuacccacccgacccgucuugaa
acacggaccaaggagucuaacacgugcgcgagucgggggcucgcacgaaa
gccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgaggu
gggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgucu
cgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccga
aagauggugaacuaugccugggcagggcgaagccagaggaaacucuggug
gagguccguagcgguccugacgugcaaaucggucguccgaccuggguaua
ggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaaguuu
cccucaggauagcuggcgcucucgcagacccgaacgcaguuuuauccggu
aaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauucuc
aaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcgug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucgagaguggacgggagcggccccgcggacgcuacgccgcgacgag
uaggagggccgcugcggugagccuugaagccuagggcgcgggcccgggug
gagccgccgcaggugcagaucuuggugguaguagcaaauauucaaacgag
aacuuugaaggccgaaguggagaaggguuccaugugaacagcaguugaac
augggucagucgguccugagagaugggcgagcgccguuccgaagggacgg
gcgauggccuccguugcccucggccgaucgaaagggagucggguucagau
ccccgaauccggagcggagaugggcgccgcgaggcguccagugcgguaac
gcgaccgaucccggagaagccggcgggagccccggggagaguucucuuuu
cuuugugaagggcagggcgcccuggaauggguucgccccgagagaggggc
ccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgc
uggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgua
cccauauccgcagcaggucuccaaggugaacagccucuggcauguuggaa
caauguagguaagggaagucggcaagccggauccguaacuucgggauaag
gauuggcucuaagggcugguagcagccgacuuagaacuggugcggaccag
gggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgg
guguugacgcgaugugauuucugcccagugcucugaaugucaaagugaag
aaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaa
gguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaagagacaugagagguguagaauaagugggaggc
ccgggccgccggugaaauaccacuacucugaucguuuuuucacugacccg
gugaggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcg
cccggccgcgcgccggccgggcgcgacccgcuccggggacagugccaggu
ggggaguuugacuggggcgguacaccugucaaacgguaacgcaggugucc
uaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaa
agcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcgggg
ccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaa
guuaccacagggauaacuggcuuguggcggccaagcguucauagcgacgu
cgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaau
ucaccaagcguuggauuguucacccacuaauagggaacgugagcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugauguguuguug
ccaugguaauccugcucaguacgagaggaaccgcagguucagacauuugg
uguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggga
uuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauacg
gcagcgccgcggagccucgguuggccucggauagccggucccccgccggg
guccggugcggagugcccuucguccugggaaacggggcgcggccggagag
gcggccgcccccucgcccgucacgcaccgcacguucguggggaaccuggc
gcuaaaccauucguagacgaccugcuucugggucgggguuucguacguag
cagagcagcucccucgcugcgaucuauugaaagucagcccucgacacaag
gguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g61 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.94 Å
• Binding residue (original residue number in PDB): S2 S3 H4 K5 F7 K10 L13 Q17 P22 I35 R36 Y37 N38 S39 K40 R41 R42 H43 W44 R45 T47 K48 L49 L51
• Binding residue (residue number reindexed from 1): S1 S2 H3 K4 F6 K9 L12 Q16 P21 I34 R35 Y36 N37 S38 K39 R40 R41 H42 W43 R44 T46 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:8g61, PDBe:8g61, PDBj:8g61
• PDBsum: 8g61
• PubMed: 37020024
• UniProt: P62891|RL39_HUMAN Large ribosomal subunit protein eL39 (Gene Name=RPL39)