Structure of PDB 8g61 Chain LM Binding Site BS01

Receptor Information

>8g61 Chain LM (length=136) Species: 9606 (Homo sapiens)

VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMP
FKCMQLTDFILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERK
AKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALLK

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

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

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): F3 R4 R5 F17 P19 H20 D29 Q33 N34 Q44 V45 R46 Q48 K53 Q56 P65 H66 H69 Q70 K71 Y72 R74 W91 K94 K101 M113 K114 K117 M118 N120 R121 K128 K132
• Binding residue (residue number reindexed from 1): F2 R3 R4 F16 P18 H19 D28 Q32 N33 Q43 V44 R45 Q47 K52 Q55 P64 H65 H68 Q69 K70 Y71 R73 W90 K93 K100 M112 K113 K116 M117 N119 R120 K127 K131

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin 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:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g61, PDBe:8g61, PDBj:8g61
• PDBsum: 8g61
• PubMed: 37020024
• UniProt: P50914|RL14_HUMAN Large ribosomal subunit protein eL14 (Gene Name=RPL14)