Structure of PDB 7nwg Chain Y3 Binding Site BS01

Receptor Information

>7nwg Chain Y3 (length=132) Species: 9986 (Oryctolagus cuniculus)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEK

Ligand information

>7nwg Chain 51 (length=3626)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugcgccgcgcucuccccccucgggggggccgggccaccccucc
cacggcgcgaccgcucucccacccggggggcggggcggacuguccccagu
gcgccccgggcgggucgcgccgucgggcccgggggagguucucucggggc
cacgcgagcgcacggggucggcggcgaugucggcuacccacccgacccgu
cuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcuacg
aaagccgccguggcgcaaugaaggugaaggccggcggcgcgccgccggcc
gaggugggaucccgaggccuuccaguccgccgagggcgcaccaccggccc
gucucgcccgccgcgccggggagguggagcacgagcgcacguguuaggac
ccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacucu
gguggagguccguagcgguccugacgugcgaaucggucguccgaccuggg
uauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccaaa
guuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcga
augauuagaggucuuggggccgaaacgaucucaaccuauucucaaacuuu
aaauggguaagaagcccggcucgcugguguggagccgggcguggaaugcg
agugccuagugggccacuuuugguaagcagaacuggcgcugcgggaugaa
ccgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccagaa
aagguguugguugauauagacagcaggaugguggccauggaagucggaau
ccgcuaaggaguguguaacaacucaccugccgaaucaacuagcccugaaa
auggauggcgcuggagcgucgggcccauacccggccgucgcuggcagucg
gcagagcgagaaagagaguggcgcggacgcuacgccgcgacgaguaggag
ggccgcugcggugagccuugaagccuagggcgcgggcccggguggagccg
ccgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuu
gaaggccgaaguggagaaggguuccaugugaacagcaguugaacaugggu
cagucgguccugagagaugggcgagcgccguuccgaagggacgggcgaug
gccuccguugcccucagccgaucgaaagggagucggguucagauccccga
auccggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcg
accgaucccggagaagccggcgggagccccggggagaguucucuuuucuu
ugugaagggcagggcgcccuggaauggguucgccccgagagaggggcccg
ugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcugg
cccuugaaaauccgggggagaggguguaaaucucgcgccgggccguaccc
auauccgcagcaggucuccaaggugaacagccucuggcauguuggaacaa
uguagguaagggaagucggcaagccggauccguaacuucgggauaaggau
uggcucuaagggcuggcagccgacuuagaacuggugcggaccaggggaau
ccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguug
acgcgaugugauuucugcccagugcucugaaugucaaagugaagaaauuc
aaugaagcgcggguaaacggcgggaguaacuaugacucucuuaagguagc
caaaugccucgucaucuaauuagugacgcgcaugaauggaugaacgagau
ucccacugucccuaccuacuauccagcgaaaccacagccaagggaacggg
cuuggcggaaucagcggggaaagaagacccuguugagcuugacucuaguc
uggcacggugaagagacaugagagguguagaauaagugggaggcccgggc
cgccggugaaauaccacuacucugaucguuuuuucacugacccggugagg
cgggggggcgagccgggcucucgcuucuggcgccaagcgcccggccggcc
gggcgcgacccgcuccggggacagugccagguggggaguuugacuggggc
gguacaccugucaaacgguaacgcagguguccuaaggcgagcucagggag
gacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugau
uuucaguacgaauacagaccgugaaagcggggccucacgauccuucugac
cuuuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacu
ggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucga
ugucggcucuuccuaucauugugaagcagaauucaccaagcguuggauug
uucacccacuaauagggaacgugagcuggguuuagaccgucgugagacag
guuaguuuuacccuacugaugauguguuguugccaugguaauccugcuca
guacgagaggaaccgcagguucagacauuugguguaugugcuuggcugag
gagccaauggggcgaagcuaccaucugugggauuaugacugaacgccucu
aagucagaaucccgcccaggcggaacgauagcgccggagccucgguuggc
cucggauagccggucccccgcccgggguccggugcggagagcccuucguc
ccgggaaacggggcggccggaaagggggccgcccucucgcccgucacgca
ccgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugcu
ucugggucgggguuucguacguagcagagcagcugcugcgaucuauugaa
agucagcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
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....>>>>.....((......<<<.....))>>>...>.>>>>>>>...>
>>..>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...(((((..<<<<<<)))))..]]]........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.........<<<<<<<<<<....<<<<<<<.<<<...<<<<<<<
.<<<<<<<<<......>>>>>>>>>>>>>>>>..>>>>>>>...>>>.>>
>>>>>>>>..........>>>.>>>>>...<<<<<<<.<<<<<<<<<<.<
<<<.........<..<<<<<<<......<<<<<<<<.>>>>>>>>.....
..>>>>>>>...>............>>>>...>>>>>>>>>>.....<..
.......>.........<...<<<<<<..>>>>>>.....<<..<<<.<<
<<<<<<<<<<<<<<....<..<<..>>.>.<<<<<<<.<<........>>
.>>>>>>>.>>>.>>>>>>>>>>.>>>...>>>.............>>..
.......>.........>>.>>>>>....>>>>...>>>>>>>>...<<<
........>>>.<<<<<<....<<<.<<<<<<<<<..<<<...<<<<...
..>>>>.....>>>...<<....>>...<<<<<.<<<<..>>>>.>>>>>
..<<<<<...<<<..<<........[...>>..>>>....>>>>>.<<<<
<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>.>>>..<
<.<..<<<<<<<.....<<<<<<<<<..<<<....<.<<<<......>>>
>.>.....>>>...<<<..<..<<........>>.>.>>>....>>>>>>
>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<<...
.<.<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<<....<<<...
.<<<....<<<..<<<<.............>>>>>>>....>>>...>>>
....>>>>>>...<<<<<<<<<.<......>>>>>>>>>>....>>>>>>
>>>>>>.>>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......
>>>...<<<<<<<...<<<(((.......<<<<<.....<<.........
.<<<.<<<..<<<.........<<<.........<<.........>>...
............<<......>>.....>>>.....>>>..>>>>>>....
......))).>>...>>>>>..>>>...>>>>>>><<<<<<.<<<.....
................]................>>>>>>>>>....>>>>
>>.<<<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>
>>>>>>.>>.....>>>>>><<<....<<.....<<<<<<.......>>>
>>>.<<<......<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<....<<<....>>>.............<<<<<<<<
<...>>>>>>>>>........>>....>>>..<<<<<........>>>>>
))<<<<....<<<......<<<<<......>>>>>....<<<....>>>.
......<<<<<<...<<<<<<<<<<<<<<<<<<<<<<<..{{{..>>>>>
>.....<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>.
.>>>>......<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>
>.........>>>>>>.................>>>.>>>>.>>>..>>.
....<<......>>>>>>..<<<<.....>>>>..>>>....<<<<....
.<<<<<<<.<<...............<<<<<...............>>>>
><<.<<<<<<<<<<<.>>>>>..>>>>>>.>>............<<<<<<
<<<..<<...........>>..<<<<<<<....<<<<.....>>>>....
..>>>>>>>....<..<<<..<<<<<<....<<<.....<<<<....>>>
>.....>>>.>>>>..>>>>>...<<.........>>...........<.
..........<<<<<.......>>>>>.....>.....>.....>>.>>>
>>>>.....>>.>>>>>>>..>>>>>>...>>>....<<<<.........
.>>>>.....[[[[..{{{.{{......[[[[....[[[..<<<<..<<<
<<<<<<.<<<<<<....<<.<<<<..........<<<.<...<<<..>>>
.............>.>>>.>>>>.>>.....>>>>>>...<<<<<.....
<<<<.....<........>..................<<<<<<<<..>>>
>>>>>...>>>>..>>>>>....>>>>>>>>>...>>>>...<<<.....
>>>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<
<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<.<<<
<<.......>>>>.>>>>.<<<....>>>.>>)))]......((((((..
(((..>>>>>>.)))))))))..........]]].....]]]].......
<<.<.<.<<<<<<...<.........>...>>>>>>...>>.>.>.....
..<<<<<.<<<<<...<...<<<<<......>>>>>.....>.<<<....
.....>>>......>>>>..>...>>>.>>....<<<.<<<....>>>..
>>>....}}..}}}.]]]]......<<<<<<....<<<..<.<<<<<...
..............>>>>>.><<<<.....<<<....<<..<.<<<.}}}
..>>>....>.>>...>>>....>>>><<<<....<<<<...........
..>>>>....>>>>.>>>.....>>>>>>.<<<<<<<..<<<.....<<<
........<<<<<<..<<<<..>>>>>.>>>>>.......>>>...<<<.
.<<<<....<<<.<<<<<........>>>>>..>>>...>>>>..>>>..
.............>>>..>>.>>>>>.<<<<<.<.............>..
..<<.<<<<<<<.<<.....<<<<.<..<<<<<.>>>>>..>>>>>....
>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7nwg Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 T8 S9 K13 K28 K36 R45 S46 R59 H61 K63 R87 K89 K103 R121 S125 K132
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 T8 S9 K13 K28 K36 R45 S46 R59 H61 K63 R87 K89 K103 R121 S125 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:7nwg, PDBe:7nwg, PDBj:7nwg
• PDBsum: 7nwg
• PubMed: 34157102
• UniProt: G1SQH0|RL26_RABIT Large ribosomal subunit protein uL24 (Gene Name=RPL26)