Structure of PDB 3j6y Chain 79 Binding Site BS01

Receptor Information

>3j6y Chain 79 (length=50) Species: 580240 (Saccharomyces cerevisiae W303)

AAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI

Ligand information

>3j6y Chain 2S (length=3308)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cucgcauuucacuggccagcaucaguuuugguggcaggauaaauccauag
gaauguagcuugccucgguaaguauuauagccugugggaauacugccagc
ugggacugaggacugcgacguaagucaaggaugcuggcauaaugguuaua
ugccgcccgucuugaaacacggaccaaggagucuaacgucuaugcgagug
uuuggguguaaaacccauacgcguaaugaaagugaacguagguuggggcc
ucgcaagaggugcacaaucgaccgauccugaugucuucggauggauuuga
guaagagcauagcuguugggacccgaaagauggugaacuaugccugaaua
gggugaagccagaggaaacucugguggaggcucguagcgguucugacgug
caaaucgaucgucgaauuuggguauaggggcgaaagacuaaucgaaccau
cuaguagcugguuccugccgaaguuucccucaggauagcagaagcucgua
ucaguuuuaugagguaaagcgaaugauuagagguuccggggucgaaauga
ccuugaccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaa
uugaacguggacauuugaaugaagagcuuuuagugggccauuuuugguaa
gcagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccggaa
uacacgcucaucagacaccacaaaagguguuaguucaucuagacagccgg
acgguggccauggaagucggaauccgcuaaggaguguguaacaacucacc
ggccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccua
uacucuaccgucaggguugauaugaugcccugacgaguaggcaggcgugg
aggucagugacgaagccuagaccguaaggucgggucgaacggccucuagu
gcagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacug
aaguggggaaagguuccacgucaacagcaguuggacguggguuagucgau
ccuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggcca
ccaucgaaagggaauccgguuaagauuccggaaccuggauauggauucuu
cacgguaacguaacugaauguggagacgucggcgcgagcccugggaggag
uuaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccggag
auggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugcg
cuugugacggcccgugaaaauccacaggaaggaauaguuuucaugccagg
ucguacugauaaccgcagcaggucuccaaggugaacagccucuaguugau
agaauaauguagauaagggaagucggcaaaauagauccguaacuucggga
uaaggauuggcucuaagggucggguagugagggccuuggucagacgcagc
gggccuuguuguagacggccuugguaggucucuuguagaccgucgcuugc
uacaacgaucaacuuagaacugguacggacaaggggaaucugacugucua
auuaaaacauagcauugcgauggucagaaagugauguugacgcaauguga
uuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcg
gguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucg
ucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
agagacauagaggguguagaauaagugggagcuucggcgccagugaaaua
ccacuaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauu
cauuuuccacguucuagcauucaaggucccauucggggcugauccggguu
gaagacauugucagguggggaguuuggcuggggcggcacaucuguuaaac
gauaacgcagauguccuaaggggggcucauggagaacagaaaucuccagu
agaacaaaaggguaaaagcccccuugauuuugauuuucagugugaauaca
aaccaugaaaguguggccuaucgauccuuuagucccucggaauuugaggc
uagaggugccagaaaaguuaccacagggauaacuggcuuguggcagucaa
gcguucauagcgacauugcuuuuugauucuucgaugucggcucuuccuau
cauaccgaagcagaauucgguaagcguuggauuguucacccacuaauagg
gaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguu
cauucggauaauugguuuuugcggcugucugaucaggcauugccgcgaag
cuaccauccgcuggauuauggcugaacgccucuaagucagaauccaugcu
agaacgcggugauuucuuugcuccacacaauauagauggauacgaauaag
gcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuug
gcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgug
gggauaaaucauuuguauacgacuuagauguacaacgggguauuguaagc
aguagaguagccuuguuguuacgaucugcugagauuaagccuuuguuguc
ugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j6y Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center.
• Resolution: 6.1 Å
• Binding residue (original residue number in PDB): A2 A3 Q4 K5 K10 M13 P22 Y37 A39 W44 R45 K48 M49
• Binding residue (residue number reindexed from 1): A1 A2 Q3 K4 K9 M12 P21 Y36 A38 W43 R44 K47 M48

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j6y, PDBe:3j6y, PDBj:3j6y
• PDBsum: 3j6y
• PubMed: 24927574
• UniProt: P04650|RL39_YEAST Large ribosomal subunit protein eL39 (Gene Name=RPL39)