Structure of PDB 8scb Chain Y Binding Site BS01

Receptor Information

>8scb Chain Y (length=134) Species: 9986 (Oryctolagus cuniculus)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>8scb Chain 5 (length=3530)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccaccccggcgccggggggcccaaguccuucuga
ucgaggcccagcccguggacggugugaggccgguagcggcccccggcgcg
ccgggcccgggucuucccggagucggguugcuugggaaugcagcccaaag
cgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguc
aacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaa
gagggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgc
ccggaggauucaacccggcggcgcgguccggccgugccggcggggcggau
cucccgcucccgucggcgggggaccgccccccggccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggccccggcggggaagguggcccgggggccccggguguuacag
ccccgccccggcagcagcagcucgccgaaucccggggccgagggagcgag
acccgugcgccgcgcucuccccccucgggggggccgggccaccccuccca
cggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgc
cgucgggcccggggggccacgcgagcgcacggggucggcggcgaugucgg
cuacccacccgacccgucuugaaacacggaccaaggagucuaacacgugc
gcgagucgggggcuacgaaagccgccguggcgcaaugaaggugaaggccg
gcggcgcgccgccggccgaggugggaucccgaggccuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcgaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccaaaguuucccucaggauagcuggcgcucuccgcaguu
uuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaa
ccuauucucaaacuuuaaauggguaagaagcccggcucgcugguguggag
ccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaaua
uucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaaca
gcaguugaacaugggucagucgguccugagagaugggcgagcgccguucc
gaagggacgggcgauggccuccguugcccucagccgaucgaaagggaguc
ggguucagauccccgaauccggaguggcggagaugggcgccgcgaggcgu
ccagugcgguaacgcgaccgaucccggagaagccggcgggagccccgggg
agaguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcc
ccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcgucc
ggugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucuc
gcgccgggccguacccauauccgcagcaggucuccaaggugaacagccuc
uggcauguuggaacaauguagguaagggaagucggcaagccggauccgua
acuucgggauaaggauuggcucuaagggcuggcagccgacuuagaacugg
ugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaagg
cccgcggcggguguugacgcgaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaug
acucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaug
aauggaugaacgagauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguu
gagcuugacucuagucuggcacggugaagagacguuuuuucacugacccg
gugaggcgggggggcgagccgggcucucgcuucuggcgccaagcgcccgg
ccggccgggcgcgacccgcuccggggacagugccagguggggaguuugac
uggggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcuc
agggaggacagaaaccucccguggagcagaagggcaaaagcucgcuugau
cuugauuuucaguacgaauacagaccgugaaagcggggccucacgauccu
ucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacaggg
auaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauagcgccggagccucg
guuggccucggauagccggucccccgccgggguccggugcggagagcccu
ucgucccgggaaacgggcggccggaaagggggccgcccucucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcugcugcgaucuau
ugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8scb Structure and consequences of eRF1 glued to the ribosomal decoding center
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 T8 S9 R11 K13 N14 R15 R17 H18 K28 S31 P33 R39 R45 S46 R59 G60 H61 K63 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 K132
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 T8 S9 R11 K13 N14 R15 R17 H18 K28 S31 P33 R39 R45 S46 R59 G60 H61 K63 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126 K132

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8scb, PDBe:8scb, PDBj:8scb
• PDBsum: 8scb
• PubMed: 38172604
• UniProt: G1SQH0|RL26_RABIT Large ribosomal subunit protein uL24 (Gene Name=RPL26)