Structure of PDB 8g60 Chain LI Binding Site BS01

Receptor Information

>8g60 Chain LI (length=208) Species: 9606 (Homo sapiens)

GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGH
MVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINK
MLSCAQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAK
FKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPSRGPL
DKWRALHS

Ligand information

>8g60 Chain L5 (length=3637)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggggggaccgucccccgaccggcgaccggccgccgc
cgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggcu
gggaaggcccggcggggaagguggcucgggggcccccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccugggggggccgggccaccccucccacggcgcg
accgcucgggcggacuguccccagugcgccccgggcgggucgcgccgucg
ggcccggggggccacgcgcgcguccccggggacggcggagcgagcgcacg
gggucggcggcgacgucggcuacccacccgacccgucuugaaacacggac
caaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgu
ggcgcaaugaaggugaaggccggcgcgcucgccggccgaggugggauccc
gaggccucuccaguccgccgagggcgcaccaccggcccgucucgcccgcc
gcgccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaacuaugccugggcagggcgaagccagaggaaacucugguggagguccg
uagcgguccugacgugcaaaucggucguccgaccuggguauaggggcgaa
agacuaaucgaaccaucuaguagcugguucccuccgaaguuucccucagg
auagcuggcgcucucgcagacccgaacgcaguuuuauccgguaaagcgaa
ugauuagaggucuuggggccgaaacgaucucaaccuauucucaaacuuua
aauggguaagaagcccggcucgcuggcguggagccgggcguggaaugcga
gugccuagugggccacuuuugguaagcagaacuggcgcugcgggaugaac
cgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccagaaa
agguguugguugauauagacagcaggacgguggccauggaagucggaauc
cgcuaaggaguguguaacaacucaccugccgaaucaacuagcccugaaaa
uggauggcgcuggagcgucgggcccauacccggccgucgccggcagucga
gaguggacgggagcgcgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
agcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauccc
ggagaagccggcgggagccccggggagaguucucuuuucuuugugaaggg
cagggcgcccuggaauggguucgccccgagagaggggcccgugccuugga
aagcgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaa
auccgggggagaggguguaaaucucgcgccgggccguacccauauccgca
gcaggucuccaaggugaacagccucuggcauguuggaacaauguagguaa
gggaagucggcaagccggauccguaacuucgggauaaggauuggcucuaa
gggcuggguagcagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuccca
cugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuugg
cggaaucagcggggaaagaagacccuguugagcuugacucuagucuggca
cggugaagagacaugagagguguagaauaagugggaggcccgggccgccg
gugaaauaccacuacucugaucguuuuuucacugacccggugaggcgggg
gggcgagccccgaggggcucucgcuucuggcgccaagcgcccggcgccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccggucccccgccgggguccggugcggagugcccuu
cguccugggaaacggggcgcggccggagaggcggccgcccccucgcccgu
cacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacga
ccugcuucugggucgggguuucguacguagcagagcagcucccucgcugc
gaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g60 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.54 Å
• Binding residue (original residue number in PDB): R3 R4 P5 A6 R7 C8 K13 N14 K15 P16 Y17 F22 R24 D35 K39 S61 E63 A64 A67 K74 R90 H92 F94 R98 N100 M102 Q112 G114 M115 R116 G117 A118 F119 G120 Q133 R154 F157 K158 P160 R162 D193 G194 K198
• Binding residue (residue number reindexed from 1): R2 R3 P4 A5 R6 C7 K12 N13 K14 P15 Y16 F21 R23 D34 K38 S60 E62 A63 A66 K73 R89 H91 F93 R97 N99 M101 Q106 G108 M109 R110 G111 A112 F113 G114 Q127 R148 F151 K152 P154 R156 D187 G188 K192

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045182 translation regulator activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0043066 negative regulation of apoptotic process
• GO:1990403 embryonic brain development

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005790 smooth endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g60, PDBe:8g60, PDBj:8g60
• PDBsum: 8g60
• PubMed: 37020024
• UniProt: P27635|RL10_HUMAN Large ribosomal subunit protein uL16 (Gene Name=RPL10)