Structure of PDB 3j6x Chain 71 Binding Site BS01

Receptor Information

>3j6x Chain 71 (length=109) Species: 580240 (Saccharomyces cerevisiae W303)

LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAP
ELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKG
LQTVVVEED

Ligand information

>3j6x 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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.>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j6x 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): R10 N15 K18 H21 G22 V23 F25 K34 R50 L51 N56 W60 R62 V64 Y69 R70 K102 G103 Q105 V108
• Binding residue (residue number reindexed from 1): R7 N12 K15 H18 G19 V20 F22 K31 R47 L48 N53 W57 R59 V61 Y66 R67 K99 G100 Q102 V105

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity

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:3j6x, PDBe:3j6x, PDBj:3j6x
• PDBsum: 3j6x
• PubMed: 24927574
• UniProt: P0C2H8|RL31A_YEAST Large ribosomal subunit protein eL31A (Gene Name=RPL31A)