Structure of PDB 3j6y Chain 59 Binding Site BS01

Receptor Information

>3j6y Chain 59 (length=188) Species: 580240 (Saccharomyces cerevisiae W303)

ANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIV
KKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRV
LRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQR
EKALNEEAEARRLKNRAARDRRAQRVAEKRDALLKEDA

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

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 N3 K8 L10 G18 K19 R20 K21 W23 L24 S37 R38 K43 K46 T56 H58 S59 K60 S61 R62 R64 R71 R74 H75 G77 Y78 G79 K80 R81 K82 G83 T84 R88 L89 P90 Q92 W95 R97 L99 R100 R103 R104 K117 H118 Y120 H121 Y124 K125 E126 K128 G129 H134 K135 R136
• Binding residue (residue number reindexed from 1): A1 N2 K7 L9 G17 K18 R19 K20 W22 L23 S36 R37 K42 K45 T55 H57 S58 K59 S60 R61 R63 R70 R73 H74 G76 Y77 G78 K79 R80 K81 G82 T83 R87 L88 P89 Q91 W94 R96 L98 R99 R102 R103 K116 H117 Y119 H120 Y123 K124 E125 K127 G128 H133 K134 R135

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

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: P0CX82|RL19A_YEAST Large ribosomal subunit protein eL19A (Gene Name=RPL19A)