Structure of PDB 8glp Chain LV Binding Site BS01

Receptor Information

>8glp Chain LV (length=133) Species: 9606 (Homo sapiens)

GSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGV
GDMVMATVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVN
NKGEMKGSAITGPVAKECADLWPRIASNAGSIA

Ligand information

>8glp Chain L5 (length=3546)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggcgggggaccgucccccgaccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccugggggggccgggccaccccucccacggcg
cgaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgcgcgucccccgaagagggggacggcggag
cgagcgcacggggucggcggcgacgucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgag
gugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcagacccgagccacgcaguuuuau
ccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcaggaaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagccccgcggacgcuacgccgc
gacgaguaggagggccgcugcggugagccuugaagccuagggcgcgggcc
cggguggagccgccgcaggugcagaucuuggugguaguagcaaauauuca
aacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcag
uugaacaugggucagucgguccugagagaugggcgagcgccguuccgaag
ggacgggcgauggccuccguugcccucggccgaucgaaagggagucgggu
ucagauccccgaauccggagcggagaugggcgccgcgaggcguccagugc
gguaacgcgaccgaucccggagaagccggcgggagccccggggagaguuc
ucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagag
aggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggcugguagcagccgacuuagaacuggugcg
gaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccg
cggcggguguugacgcgaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacuc
ucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaaug
gaugaacgagauucccacugucccuaccuacuauccagcgaaaccacagc
caagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagc
uugacucuagucuggcacggugaagagacguuuuuucacugacccgguga
ggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugacuggggcgguacaccugucaaacgguaacgcagguguccuaag
gcgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcu
cgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggccuc
acgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguua
ccacagggauaacuggcuuguggcggccaagcguucauagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauacggcag
cgccgcggagccucgguuggccucggauagccggucccccgcgggguccg
gugcggagugcccuucguccugggaaacggggcgcggccggagaggcggc
cgcccccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaa
accauucguagacgaccugcuucugggucgggguuucguacguagcagag
cagcgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8glp mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): G8 S9 S10 A12 F14 R15 S17 G19 P21 V22 A24 V25 Y38 I40 S41 K43 G44 I45 K46 R48 L49 N50 R51 L52 M62 T64 K66 K74 V76 R85 K86 R89 F95
• Binding residue (residue number reindexed from 1): G1 S2 S3 A5 F7 R8 S10 G12 P14 V15 A17 V18 Y31 I33 S34 K36 G37 I38 K39 R41 L42 N43 R44 L45 M55 T57 K59 K67 V69 R78 K79 R82 F88

Gene Ontology

Molecular Function

• GO:0001223 transcription coactivator binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0070180 large ribosomal subunit rRNA binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006610 ribosomal protein import into nucleus
• GO:0008284 positive regulation of cell population proliferation
• GO:0010628 positive regulation of gene expression
• GO:0032986 protein-DNA complex disassembly
• GO:0050821 protein stabilization
• GO:0070314 G1 to G0 transition
• GO:0072717 cellular response to actinomycin D
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1903450 regulation of G1 to G0 transition
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8glp, PDBe:8glp, PDBj:8glp
• PDBsum: 8glp
• PubMed: 37020024
• UniProt: P62829|RL23_HUMAN Large ribosomal subunit protein uL14 (Gene Name=RPL23)